diff --git a/src/NATS.Server/JetStream/Storage/FileStore.cs b/src/NATS.Server/JetStream/Storage/FileStore.cs
index 2518520..78ae6f3 100644
--- a/src/NATS.Server/JetStream/Storage/FileStore.cs
+++ b/src/NATS.Server/JetStream/Storage/FileStore.cs
@@ -10,23 +10,34 @@ using ApiStreamState = NATS.Server.JetStream.Models.ApiStreamState;
 
 namespace NATS.Server.JetStream.Storage;
 
+/// <summary>
+/// Block-based file store for JetStream messages. Uses <see cref="MsgBlock"/> for
+/// on-disk persistence and maintains an in-memory cache (<see cref="StoredMessage"/>)
+/// for fast reads and subject queries.
+///
+/// Reference: golang/nats-server/server/filestore.go — block manager, block rotation,
+/// recovery via scanning .blk files, soft-delete via dmap.
+/// </summary>
 public sealed class FileStore : IStreamStore, IAsyncDisposable
 {
     private readonly FileStoreOptions _options;
-    private readonly string _dataFilePath;
-    private readonly string _manifestPath;
+
+    // In-memory cache: keyed by sequence number. This is the primary data structure
+    // for reads and queries. The blocks are the on-disk persistence layer.
     private readonly Dictionary<ulong, StoredMessage> _messages = new();
-    private readonly Dictionary<ulong, BlockPointer> _index = new();
+
+    // Block-based storage: the active (writable) block and sealed blocks.
+    private readonly List<MsgBlock> _blocks = [];
+    private MsgBlock? _activeBlock;
+    private int _nextBlockId;
+
     private ulong _last;
-    private int _blockCount;
-    private long _activeBlockBytes;
-    private long _writeOffset;
 
     // Resolved at construction time: which format family to use.
-    private readonly bool _useS2;       // true → S2Codec (FSV2 compression path)
-    private readonly bool _useAead;     // true → AeadEncryptor (FSV2 encryption path)
+    private readonly bool _useS2;       // true -> S2Codec (FSV2 compression path)
+    private readonly bool _useAead;     // true -> AeadEncryptor (FSV2 encryption path)
 
-    public int BlockCount => _messages.Count == 0 ? 0 : Math.Max(_blockCount, 1);
+    public int BlockCount => _blocks.Count;
     public bool UsedIndexManifestOnStartup { get; private set; }
 
     public FileStore(FileStoreOptions options)
@@ -40,10 +51,10 @@ public sealed class FileStore : IStreamStore, IAsyncDisposable
         _useAead = _options.Cipher != StoreCipher.NoCipher;
 
         Directory.CreateDirectory(options.Directory);
-        _dataFilePath = Path.Combine(options.Directory, "messages.jsonl");
-        _manifestPath = Path.Combine(options.Directory, _options.IndexManifestFileName);
-        LoadBlockIndexManifestOnStartup();
-        LoadExisting();
+
+        // Attempt legacy JSONL migration first, then recover from blocks.
+        MigrateLegacyJsonl();
+        RecoverBlocks();
     }
 
     public async ValueTask<ulong> AppendAsync(string subject, ReadOnlyMemory<byte> payload, CancellationToken ct)
@@ -51,28 +62,36 @@ public sealed class FileStore : IStreamStore, IAsyncDisposable
         PruneExpired(DateTime.UtcNow);
 
         _last++;
+        var now = DateTime.UtcNow;
+        var timestamp = new DateTimeOffset(now).ToUnixTimeMilliseconds() * 1_000_000L;
         var persistedPayload = TransformForPersist(payload.Span);
         var stored = new StoredMessage
         {
             Sequence = _last,
             Subject = subject,
             Payload = payload.ToArray(),
-            TimestampUtc = DateTime.UtcNow,
+            TimestampUtc = now,
         };
         _messages[_last] = stored;
 
-        var line = JsonSerializer.Serialize(new FileRecord
+        // Write to MsgBlock. The payload stored in the block is the transformed
+        // (compressed/encrypted) payload, not the plaintext.
+        EnsureActiveBlock();
+        try
         {
-            Sequence = stored.Sequence,
-            Subject = stored.Subject,
-            PayloadBase64 = Convert.ToBase64String(persistedPayload),
-            TimestampUtc = stored.TimestampUtc,
-        });
-        await File.AppendAllTextAsync(_dataFilePath, line + Environment.NewLine, ct);
+            _activeBlock!.WriteAt(_last, subject, ReadOnlyMemory<byte>.Empty, persistedPayload, timestamp);
+        }
+        catch (InvalidOperationException)
+        {
+            // Block is sealed. Rotate to a new block and retry.
+            RotateBlock();
+            _activeBlock!.WriteAt(_last, subject, ReadOnlyMemory<byte>.Empty, persistedPayload, timestamp);
+        }
+
+        // Check if the block just became sealed after this write.
+        if (_activeBlock!.IsSealed)
+            RotateBlock();
 
-        var recordBytes = Encoding.UTF8.GetByteCount(line + Environment.NewLine);
-        TrackBlockForRecord(recordBytes, stored.Sequence);
-        PersistBlockIndexManifest(_manifestPath, _index);
         return _last;
     }
 
@@ -106,23 +125,31 @@ public sealed class FileStore : IStreamStore, IAsyncDisposable
         {
             if (sequence == _last)
                 _last = _messages.Count == 0 ? 0UL : _messages.Keys.Max();
-            RewriteDataFile();
+
+            // Soft-delete in the block that contains this sequence.
+            DeleteInBlock(sequence);
         }
+
         return ValueTask.FromResult(removed);
     }
 
     public ValueTask PurgeAsync(CancellationToken ct)
     {
         _messages.Clear();
-        _index.Clear();
         _last = 0;
-        _blockCount = 0;
-        _activeBlockBytes = 0;
-        _writeOffset = 0;
-        if (File.Exists(_dataFilePath))
-            File.Delete(_dataFilePath);
-        if (File.Exists(_manifestPath))
-            File.Delete(_manifestPath);
+
+        // Dispose and delete all blocks.
+        DisposeAllBlocks();
+        CleanBlockFiles();
+
+        // Clean up any legacy files that might still exist.
+        var jsonlPath = Path.Combine(_options.Directory, "messages.jsonl");
+        if (File.Exists(jsonlPath))
+            File.Delete(jsonlPath);
+        var manifestPath = Path.Combine(_options.Directory, _options.IndexManifestFileName);
+        if (File.Exists(manifestPath))
+            File.Delete(manifestPath);
+
         return ValueTask.CompletedTask;
     }
 
@@ -145,11 +172,11 @@ public sealed class FileStore : IStreamStore, IAsyncDisposable
     public ValueTask RestoreSnapshotAsync(ReadOnlyMemory<byte> snapshot, CancellationToken ct)
     {
         _messages.Clear();
-        _index.Clear();
         _last = 0;
-        _blockCount = 0;
-        _activeBlockBytes = 0;
-        _writeOffset = 0;
+
+        // Dispose existing blocks and clean files.
+        DisposeAllBlocks();
+        CleanBlockFiles();
 
         if (!snapshot.IsEmpty)
         {
@@ -158,11 +185,12 @@ public sealed class FileStore : IStreamStore, IAsyncDisposable
             {
                 foreach (var record in records)
                 {
+                    var restoredPayload = RestorePayload(Convert.FromBase64String(record.PayloadBase64 ?? string.Empty));
                     var message = new StoredMessage
                     {
                         Sequence = record.Sequence,
                         Subject = record.Subject ?? string.Empty,
-                        Payload = RestorePayload(Convert.FromBase64String(record.PayloadBase64 ?? string.Empty)),
+                        Payload = restoredPayload,
                         TimestampUtc = record.TimestampUtc,
                     };
                     _messages[record.Sequence] = message;
@@ -171,7 +199,8 @@ public sealed class FileStore : IStreamStore, IAsyncDisposable
             }
         }
 
-        RewriteDataFile();
+        // Write all messages to fresh blocks.
+        RewriteBlocks();
         return ValueTask.CompletedTask;
     }
 
@@ -194,144 +223,302 @@ public sealed class FileStore : IStreamStore, IAsyncDisposable
             _messages.Remove(first);
         }
 
-        RewriteDataFile();
+        // Rewrite blocks to reflect the trim (removes trimmed messages from disk).
+        RewriteBlocks();
     }
 
-    public ValueTask DisposeAsync() => ValueTask.CompletedTask;
-
-    private void LoadExisting()
+    public ValueTask DisposeAsync()
     {
-        if (!File.Exists(_dataFilePath))
+        DisposeAllBlocks();
+        return ValueTask.CompletedTask;
+    }
+
+    // -------------------------------------------------------------------------
+    // Block management
+    // -------------------------------------------------------------------------
+
+    /// <summary>
+    /// Ensures an active (writable) block exists. Creates one if needed.
+    /// </summary>
+    private void EnsureActiveBlock()
+    {
+        if (_activeBlock is null || _activeBlock.IsSealed)
+            RotateBlock();
+    }
+
+    /// <summary>
+    /// Creates a new active block. The previous active block (if any) stays in the
+    /// block list as a sealed block. The firstSequence is set to _last + 1 (the next
+    /// expected sequence), but actual sequences come from WriteAt calls.
+    /// </summary>
+    private void RotateBlock()
+    {
+        var firstSeq = _last + 1;
+        var block = MsgBlock.Create(_nextBlockId, _options.Directory, _options.BlockSizeBytes, firstSeq);
+        _blocks.Add(block);
+        _activeBlock = block;
+        _nextBlockId++;
+    }
+
+    /// <summary>
+    /// Soft-deletes a message in the block that contains it.
+    /// </summary>
+    private void DeleteInBlock(ulong sequence)
+    {
+        foreach (var block in _blocks)
+        {
+            if (sequence >= block.FirstSequence && sequence <= block.LastSequence)
+            {
+                block.Delete(sequence);
+                return;
+            }
+        }
+    }
+
+    /// <summary>
+    /// Disposes all blocks and clears the block list.
+    /// </summary>
+    private void DisposeAllBlocks()
+    {
+        foreach (var block in _blocks)
+            block.Dispose();
+        _blocks.Clear();
+        _activeBlock = null;
+        _nextBlockId = 0;
+    }
+
+    /// <summary>
+    /// Deletes all .blk files in the store directory.
+    /// </summary>
+    private void CleanBlockFiles()
+    {
+        if (!Directory.Exists(_options.Directory))
             return;
 
-        foreach (var line in File.ReadLines(_dataFilePath))
+        foreach (var blkFile in Directory.GetFiles(_options.Directory, "*.blk"))
         {
-            if (string.IsNullOrWhiteSpace(line))
+            try { File.Delete(blkFile); }
+            catch { /* best effort */ }
+        }
+    }
+
+    /// <summary>
+    /// Rewrites all blocks from the in-memory message cache. Used after trim,
+    /// snapshot restore, or legacy migration.
+    /// </summary>
+    private void RewriteBlocks()
+    {
+        DisposeAllBlocks();
+        CleanBlockFiles();
+
+        _last = _messages.Count == 0 ? 0UL : _messages.Keys.Max();
+
+        foreach (var message in _messages.OrderBy(kv => kv.Key).Select(kv => kv.Value))
+        {
+            var persistedPayload = TransformForPersist(message.Payload.Span);
+            var timestamp = new DateTimeOffset(message.TimestampUtc).ToUnixTimeMilliseconds() * 1_000_000L;
+
+            EnsureActiveBlock();
+            try
+            {
+                _activeBlock!.WriteAt(message.Sequence, message.Subject, ReadOnlyMemory<byte>.Empty, persistedPayload, timestamp);
+            }
+            catch (InvalidOperationException)
+            {
+                RotateBlock();
+                _activeBlock!.WriteAt(message.Sequence, message.Subject, ReadOnlyMemory<byte>.Empty, persistedPayload, timestamp);
+            }
+
+            if (_activeBlock!.IsSealed)
+                RotateBlock();
+        }
+    }
+
+    // -------------------------------------------------------------------------
+    // Recovery: scan .blk files on startup and rebuild in-memory state.
+    // -------------------------------------------------------------------------
+
+    /// <summary>
+    /// Recovers all blocks from .blk files in the store directory.
+    /// </summary>
+    private void RecoverBlocks()
+    {
+        var blkFiles = Directory.GetFiles(_options.Directory, "*.blk");
+        if (blkFiles.Length == 0)
+            return;
+
+        // Sort by block ID (filename is like "000000.blk", "000001.blk", ...).
+        Array.Sort(blkFiles, StringComparer.OrdinalIgnoreCase);
+
+        var maxBlockId = -1;
+
+        foreach (var blkFile in blkFiles)
+        {
+            var fileName = Path.GetFileNameWithoutExtension(blkFile);
+            if (!int.TryParse(fileName, out var blockId))
                 continue;
 
-            var record = JsonSerializer.Deserialize<FileRecord>(line);
-            if (record == null)
-                continue;
+            try
+            {
+                var block = MsgBlock.Recover(blockId, _options.Directory);
+                _blocks.Add(block);
+
+                if (blockId > maxBlockId)
+                    maxBlockId = blockId;
+
+                // Read all non-deleted records from this block and populate the in-memory cache.
+                RecoverMessagesFromBlock(block);
+            }
+            catch (InvalidDataException)
+            {
+                // InvalidDataException indicates key mismatch or integrity failure —
+                // propagate so the caller knows the store cannot be opened.
+                throw;
+            }
+            catch
+            {
+                // Skip corrupted blocks — non-critical recovery errors.
+            }
+        }
+
+        _nextBlockId = maxBlockId + 1;
+
+        // The last block is the active block if it has capacity (not sealed).
+        if (_blocks.Count > 0)
+        {
+            var lastBlock = _blocks[^1];
+            _activeBlock = lastBlock;
+        }
+
+        PruneExpired(DateTime.UtcNow);
+    }
+
+    /// <summary>
+    /// Reads all non-deleted records from a block and adds them to the in-memory cache.
+    /// </summary>
+    private void RecoverMessagesFromBlock(MsgBlock block)
+    {
+        // We need to iterate through all sequences in the block.
+        // MsgBlock tracks first/last sequence, so we try each one.
+        var first = block.FirstSequence;
+        var last = block.LastSequence;
+
+        if (first == 0 && last == 0)
+            return; // Empty block.
+
+        for (var seq = first; seq <= last; seq++)
+        {
+            var record = block.Read(seq);
+            if (record is null)
+                continue; // Deleted or not present.
+
+            // The payload stored in the block is the transformed (compressed/encrypted) payload.
+            // We need to reverse-transform it to get the original plaintext.
+            // InvalidDataException (e.g., wrong key) propagates to the caller.
+            var originalPayload = RestorePayload(record.Payload.Span);
 
             var message = new StoredMessage
             {
                 Sequence = record.Sequence,
-                Subject = record.Subject ?? string.Empty,
-                Payload = RestorePayload(Convert.FromBase64String(record.PayloadBase64 ?? string.Empty)),
-                TimestampUtc = record.TimestampUtc,
+                Subject = record.Subject,
+                Payload = originalPayload,
+                TimestampUtc = DateTimeOffset.FromUnixTimeMilliseconds(record.Timestamp / 1_000_000L).UtcDateTime,
             };
 
             _messages[message.Sequence] = message;
             if (message.Sequence > _last)
                 _last = message.Sequence;
-
-            if (!UsedIndexManifestOnStartup || !_index.ContainsKey(message.Sequence))
-            {
-                var recordBytes = Encoding.UTF8.GetByteCount(line + Environment.NewLine);
-                TrackBlockForRecord(recordBytes, message.Sequence);
-            }
         }
-
-        PruneExpired(DateTime.UtcNow);
-        PersistBlockIndexManifest(_manifestPath, _index);
     }
 
-    private void RewriteDataFile()
+    // -------------------------------------------------------------------------
+    // Legacy JSONL migration: if messages.jsonl exists, migrate to blocks.
+    // -------------------------------------------------------------------------
+
+    /// <summary>
+    /// Migrates data from the legacy JSONL format to block-based storage.
+    /// If messages.jsonl exists, reads all records, writes them to blocks,
+    /// then deletes the JSONL file and manifest.
+    /// </summary>
+    private void MigrateLegacyJsonl()
     {
-        Directory.CreateDirectory(Path.GetDirectoryName(_dataFilePath)!);
-        _index.Clear();
-        _blockCount = 0;
-        _activeBlockBytes = 0;
-        _writeOffset = 0;
-        _last = _messages.Count == 0 ? 0UL : _messages.Keys.Max();
-
-        using var stream = new FileStream(_dataFilePath, FileMode.Create, FileAccess.Write, FileShare.Read);
-        using var writer = new StreamWriter(stream, Encoding.UTF8);
-
-        foreach (var message in _messages.OrderBy(kv => kv.Key).Select(kv => kv.Value))
-        {
-            var line = JsonSerializer.Serialize(new FileRecord
-            {
-                Sequence = message.Sequence,
-                Subject = message.Subject,
-                PayloadBase64 = Convert.ToBase64String(TransformForPersist(message.Payload.Span)),
-                TimestampUtc = message.TimestampUtc,
-            });
-
-            writer.WriteLine(line);
-            var recordBytes = Encoding.UTF8.GetByteCount(line + Environment.NewLine);
-            TrackBlockForRecord(recordBytes, message.Sequence);
-        }
-
-        writer.Flush();
-        PersistBlockIndexManifest(_manifestPath, _index);
-    }
-
-    private void LoadBlockIndexManifestOnStartup()
-    {
-        if (!File.Exists(_manifestPath))
+        var jsonlPath = Path.Combine(_options.Directory, "messages.jsonl");
+        if (!File.Exists(jsonlPath))
             return;
 
-        try
-        {
-            var manifest = JsonSerializer.Deserialize<IndexManifest>(File.ReadAllText(_manifestPath));
-            if (manifest is null || manifest.Version != 1)
-                return;
+        // Read all records from the JSONL file.
+        var legacyMessages = new List<(ulong Sequence, string Subject, byte[] Payload, DateTime TimestampUtc)>();
 
-            _index.Clear();
-            foreach (var entry in manifest.Entries)
-                _index[entry.Sequence] = new BlockPointer(entry.BlockId, entry.Offset);
-
-            _blockCount = Math.Max(manifest.BlockCount, 0);
-            _activeBlockBytes = Math.Max(manifest.ActiveBlockBytes, 0);
-            _writeOffset = Math.Max(manifest.WriteOffset, 0);
-            UsedIndexManifestOnStartup = true;
-        }
-        catch
+        foreach (var line in File.ReadLines(jsonlPath))
         {
-            UsedIndexManifestOnStartup = false;
-            _index.Clear();
-            _blockCount = 0;
-            _activeBlockBytes = 0;
-            _writeOffset = 0;
-        }
-    }
+            if (string.IsNullOrWhiteSpace(line))
+                continue;
 
-    private void PersistBlockIndexManifest(string manifestPath, Dictionary<ulong, BlockPointer> blockIndex)
-    {
-        var manifest = new IndexManifest
-        {
-            Version = 1,
-            BlockCount = _blockCount,
-            ActiveBlockBytes = _activeBlockBytes,
-            WriteOffset = _writeOffset,
-            Entries = [.. blockIndex.Select(kv => new IndexEntry
+            FileRecord? record;
+            try
             {
-                Sequence = kv.Key,
-                BlockId = kv.Value.BlockId,
-                Offset = kv.Value.Offset,
-            }).OrderBy(e => e.Sequence)],
-        };
+                record = JsonSerializer.Deserialize<FileRecord>(line);
+            }
+            catch
+            {
+                continue; // Skip corrupted lines.
+            }
 
-        File.WriteAllText(manifestPath, JsonSerializer.Serialize(manifest));
-    }
+            if (record == null)
+                continue;
 
-    private void TrackBlockForRecord(int recordBytes, ulong sequence)
-    {
-        if (_blockCount == 0)
-            _blockCount = 1;
+            byte[] originalPayload;
+            try
+            {
+                originalPayload = RestorePayload(Convert.FromBase64String(record.PayloadBase64 ?? string.Empty));
+            }
+            catch
+            {
+                // Re-throw for integrity failures (e.g., wrong encryption key).
+                throw;
+            }
 
-        if (_activeBlockBytes > 0 && _activeBlockBytes + recordBytes > _options.BlockSizeBytes)
-        {
-            _blockCount++;
-            _activeBlockBytes = 0;
+            legacyMessages.Add((record.Sequence, record.Subject ?? string.Empty, originalPayload, record.TimestampUtc));
         }
 
-        _index[sequence] = new BlockPointer(_blockCount, _writeOffset);
-        _activeBlockBytes += recordBytes;
-        _writeOffset += recordBytes;
+        if (legacyMessages.Count == 0)
+        {
+            // Delete the empty JSONL file.
+            File.Delete(jsonlPath);
+            var manifestPath = Path.Combine(_options.Directory, _options.IndexManifestFileName);
+            if (File.Exists(manifestPath))
+                File.Delete(manifestPath);
+            return;
+        }
+
+        // Add to the in-memory cache.
+        foreach (var (seq, subject, payload, ts) in legacyMessages)
+        {
+            _messages[seq] = new StoredMessage
+            {
+                Sequence = seq,
+                Subject = subject,
+                Payload = payload,
+                TimestampUtc = ts,
+            };
+            if (seq > _last)
+                _last = seq;
+        }
+
+        // Write all messages to fresh blocks.
+        RewriteBlocks();
+
+        // Delete the legacy files.
+        File.Delete(jsonlPath);
+        var manifestFile = Path.Combine(_options.Directory, _options.IndexManifestFileName);
+        if (File.Exists(manifestFile))
+            File.Delete(manifestFile);
     }
 
+    // -------------------------------------------------------------------------
+    // Expiry
+    // -------------------------------------------------------------------------
+
     private void PruneExpired(DateTime nowUtc)
     {
         if (_options.MaxAgeMs <= 0)
@@ -349,7 +536,7 @@ public sealed class FileStore : IStreamStore, IAsyncDisposable
         foreach (var sequence in expired)
             _messages.Remove(sequence);
 
-        RewriteDataFile();
+        RewriteBlocks();
     }
 
     // -------------------------------------------------------------------------
@@ -586,22 +773,4 @@ public sealed class FileStore : IStreamStore, IAsyncDisposable
         public string? PayloadBase64 { get; init; }
         public DateTime TimestampUtc { get; init; }
     }
-
-    private readonly record struct BlockPointer(int BlockId, long Offset);
-
-    private sealed class IndexManifest
-    {
-        public int Version { get; init; }
-        public int BlockCount { get; init; }
-        public long ActiveBlockBytes { get; init; }
-        public long WriteOffset { get; init; }
-        public List<IndexEntry> Entries { get; init; } = [];
-    }
-
-    private sealed class IndexEntry
-    {
-        public ulong Sequence { get; init; }
-        public int BlockId { get; init; }
-        public long Offset { get; init; }
-    }
 }
diff --git a/src/NATS.Server/JetStream/Storage/MsgBlock.cs b/src/NATS.Server/JetStream/Storage/MsgBlock.cs
index 553210c..75d5c3d 100644
--- a/src/NATS.Server/JetStream/Storage/MsgBlock.cs
+++ b/src/NATS.Server/JetStream/Storage/MsgBlock.cs
@@ -149,7 +149,7 @@ public sealed class MsgBlock : IDisposable
     }
 
     /// <summary>
-    /// Appends a message to the block.
+    /// Appends a message to the block with an auto-assigned sequence number.
     /// </summary>
     /// <param name="subject">NATS subject.</param>
     /// <param name="headers">Optional message headers.</param>
@@ -199,6 +199,56 @@ public sealed class MsgBlock : IDisposable
         }
     }
 
+    /// <summary>
+    /// Appends a message to the block with an explicit sequence number and timestamp.
+    /// Used by FileStore when rewriting blocks from the in-memory cache where
+    /// sequences may have gaps (from prior removals).
+    /// </summary>
+    /// <param name="sequence">Explicit sequence number to assign.</param>
+    /// <param name="subject">NATS subject.</param>
+    /// <param name="headers">Optional message headers.</param>
+    /// <param name="payload">Message body payload.</param>
+    /// <param name="timestamp">Timestamp in Unix nanoseconds.</param>
+    /// <exception cref="InvalidOperationException">Block is sealed.</exception>
+    public void WriteAt(ulong sequence, string subject, ReadOnlyMemory<byte> headers, ReadOnlyMemory<byte> payload, long timestamp)
+    {
+        _lock.EnterWriteLock();
+        try
+        {
+            if (_writeOffset >= _maxBytes)
+                throw new InvalidOperationException("Block is sealed; cannot write new messages.");
+
+            var record = new MessageRecord
+            {
+                Sequence = sequence,
+                Subject = subject,
+                Headers = headers,
+                Payload = payload,
+                Timestamp = timestamp,
+                Deleted = false,
+            };
+
+            var encoded = MessageRecord.Encode(record);
+            var offset = _writeOffset;
+
+            RandomAccess.Write(_handle, encoded, offset);
+            _writeOffset = offset + encoded.Length;
+
+            _index[sequence] = (offset, encoded.Length);
+
+            if (_totalWritten == 0)
+                _firstSequence = sequence;
+
+            _lastSequence = sequence;
+            _nextSequence = Math.Max(_nextSequence, sequence + 1);
+            _totalWritten++;
+        }
+        finally
+        {
+            _lock.ExitWriteLock();
+        }
+    }
+
     /// <summary>
     /// Reads a message by sequence number. Uses positional I/O
     /// (<see cref="RandomAccess.Read"/>) so concurrent readers don't
diff --git a/tests/NATS.Server.Tests/JetStream/JetStreamFileStoreCompressionEncryptionParityTests.cs b/tests/NATS.Server.Tests/JetStream/JetStreamFileStoreCompressionEncryptionParityTests.cs
index c051a3e..812f9cf 100644
--- a/tests/NATS.Server.Tests/JetStream/JetStreamFileStoreCompressionEncryptionParityTests.cs
+++ b/tests/NATS.Server.Tests/JetStream/JetStreamFileStoreCompressionEncryptionParityTests.cs
@@ -1,5 +1,4 @@
 using System.Text;
-using System.Text.Json;
 using NATS.Server.JetStream.Storage;
 
 namespace NATS.Server.Tests;
@@ -29,10 +28,14 @@ public class JetStreamFileStoreCompressionEncryptionParityTests
                 Encoding.UTF8.GetString(loaded.Payload.ToArray()).ShouldBe("payload");
             }
 
-            var firstLine = File.ReadLines(Path.Combine(dir, "messages.jsonl")).First();
-            var payloadBase64 = JsonDocument.Parse(firstLine).RootElement.GetProperty("PayloadBase64").GetString();
-            payloadBase64.ShouldNotBeNull();
-            var persisted = Convert.FromBase64String(payloadBase64!);
+            // Block-based storage: read the .blk file to verify FSV1 envelope.
+            var blkFiles = Directory.GetFiles(dir, "*.blk");
+            blkFiles.Length.ShouldBeGreaterThan(0);
+
+            // Read the first record from the block file and verify FSV1 magic in payload.
+            var blkBytes = File.ReadAllBytes(blkFiles[0]);
+            var record = MessageRecord.Decode(blkBytes.AsSpan(0, MessageRecord.MeasureRecord(blkBytes)));
+            var persisted = record.Payload.ToArray();
             persisted.Take(4).SequenceEqual("FSV1"u8.ToArray()).ShouldBeTrue();
 
             Should.Throw<InvalidDataException>(() =>
diff --git a/tests/NATS.Server.Tests/JetStream/JetStreamFileStoreDurabilityParityTests.cs b/tests/NATS.Server.Tests/JetStream/JetStreamFileStoreDurabilityParityTests.cs
index 0b51138..cd95bf2 100644
--- a/tests/NATS.Server.Tests/JetStream/JetStreamFileStoreDurabilityParityTests.cs
+++ b/tests/NATS.Server.Tests/JetStream/JetStreamFileStoreDurabilityParityTests.cs
@@ -23,10 +23,10 @@ public class JetStreamFileStoreDurabilityParityTests
                     await store.AppendAsync("orders.created", Encoding.UTF8.GetBytes($"payload-{i}"), default);
             }
 
-            File.Exists(Path.Combine(dir, options.IndexManifestFileName)).ShouldBeTrue();
+            // Block-based storage: .blk files should be present on disk.
+            Directory.GetFiles(dir, "*.blk").Length.ShouldBeGreaterThan(0);
 
             await using var reopened = new FileStore(options);
-            reopened.UsedIndexManifestOnStartup.ShouldBeTrue();
             var state = await reopened.GetStateAsync(default);
             state.Messages.ShouldBe((ulong)1000);
             reopened.BlockCount.ShouldBeGreaterThan(1);
diff --git a/tests/NATS.Server.Tests/JetStream/Storage/FileStoreBlockTests.cs b/tests/NATS.Server.Tests/JetStream/Storage/FileStoreBlockTests.cs
new file mode 100644
index 0000000..a59931e
--- /dev/null
+++ b/tests/NATS.Server.Tests/JetStream/Storage/FileStoreBlockTests.cs
@@ -0,0 +1,289 @@
+// Reference: golang/nats-server/server/filestore_test.go
+// Tests for Task A3: FileStore Block Manager Rewrite.
+// Verifies that FileStore correctly uses MsgBlock-based storage:
+// block files on disk, block rotation, recovery, purge, snapshot,
+// soft-delete, and payload transformation (S2/AEAD) integration.
+
+using System.Text;
+using NATS.Server.JetStream.Storage;
+
+namespace NATS.Server.Tests.JetStream.Storage;
+
+public sealed class FileStoreBlockTests : IDisposable
+{
+    private readonly string _dir;
+
+    public FileStoreBlockTests()
+    {
+        _dir = Path.Combine(Path.GetTempPath(), $"nats-js-fs-block-{Guid.NewGuid():N}");
+        Directory.CreateDirectory(_dir);
+    }
+
+    public void Dispose()
+    {
+        if (Directory.Exists(_dir))
+            Directory.Delete(_dir, recursive: true);
+    }
+
+    private FileStore CreateStore(string subdirectory, FileStoreOptions? options = null)
+    {
+        var dir = Path.Combine(_dir, subdirectory);
+        var opts = options ?? new FileStoreOptions();
+        opts.Directory = dir;
+        return new FileStore(opts);
+    }
+
+    // Go: filestore.go block-based storage — verify .blk files are created on disk.
+    [Fact]
+    public async Task Append_UsesBlockStorage()
+    {
+        var subDir = "blk-storage";
+        var dir = Path.Combine(_dir, subDir);
+
+        await using var store = CreateStore(subDir);
+
+        await store.AppendAsync("foo", "Hello World"u8.ToArray(), default);
+
+        // At least one .blk file should exist in the store directory.
+        var blkFiles = Directory.GetFiles(dir, "*.blk");
+        blkFiles.Length.ShouldBeGreaterThanOrEqualTo(1);
+
+        // The old JSONL file should NOT exist.
+        File.Exists(Path.Combine(dir, "messages.jsonl")).ShouldBeFalse();
+    }
+
+    // Go: filestore.go block rotation — rbytes check causes new block creation.
+    [Fact]
+    public async Task MultiBlock_RotatesWhenFull()
+    {
+        var subDir = "blk-rotation";
+        var dir = Path.Combine(_dir, subDir);
+
+        // Small block size to force rotation quickly.
+        await using var store = CreateStore(subDir, new FileStoreOptions { BlockSizeBytes = 256 });
+
+        // Write enough messages to exceed 256 bytes per block.
+        for (var i = 0; i < 20; i++)
+            await store.AppendAsync("foo", "Hello World - block rotation test!"u8.ToArray(), default);
+
+        var state = await store.GetStateAsync(default);
+        state.Messages.ShouldBe((ulong)20);
+
+        // Multiple .blk files should be created.
+        var blkFiles = Directory.GetFiles(dir, "*.blk");
+        blkFiles.Length.ShouldBeGreaterThan(1);
+
+        // BlockCount should reflect multiple blocks.
+        store.BlockCount.ShouldBeGreaterThan(1);
+    }
+
+    // Go: filestore.go multi-block load — messages span multiple blocks.
+    [Fact]
+    public async Task Load_AcrossBlocks()
+    {
+        var subDir = "blk-across";
+
+        // Small block size to force multiple blocks.
+        await using var store = CreateStore(subDir, new FileStoreOptions { BlockSizeBytes = 256 });
+
+        for (var i = 0; i < 20; i++)
+            await store.AppendAsync("foo", Encoding.UTF8.GetBytes($"msg-{i:D4}"), default);
+
+        // Verify we have multiple blocks.
+        store.BlockCount.ShouldBeGreaterThan(1);
+
+        // All messages should be loadable, regardless of which block they are in.
+        for (ulong i = 1; i <= 20; i++)
+        {
+            var msg = await store.LoadAsync(i, default);
+            msg.ShouldNotBeNull();
+            msg!.Subject.ShouldBe("foo");
+            var expected = Encoding.UTF8.GetBytes($"msg-{(int)(i - 1):D4}");
+            msg.Payload.ToArray().ShouldBe(expected);
+        }
+    }
+
+    // Go: filestore.go recovery — block files are rescanned on startup.
+    [Fact]
+    public async Task Recovery_AfterRestart()
+    {
+        var subDir = "blk-recovery";
+        var dir = Path.Combine(_dir, subDir);
+
+        // Write data and dispose.
+        await using (var store = CreateStore(subDir, new FileStoreOptions { BlockSizeBytes = 256 }))
+        {
+            for (var i = 0; i < 20; i++)
+                await store.AppendAsync("foo", Encoding.UTF8.GetBytes($"msg-{i:D4}"), default);
+
+            var state = await store.GetStateAsync(default);
+            state.Messages.ShouldBe((ulong)20);
+        }
+
+        // .blk files should still exist after dispose.
+        var blkFiles = Directory.GetFiles(dir, "*.blk");
+        blkFiles.Length.ShouldBeGreaterThan(0);
+
+        // Recreate FileStore from the same directory.
+        await using (var store = CreateStore(subDir, new FileStoreOptions { BlockSizeBytes = 256 }))
+        {
+            var state = await store.GetStateAsync(default);
+            state.Messages.ShouldBe((ulong)20);
+            state.FirstSeq.ShouldBe((ulong)1);
+            state.LastSeq.ShouldBe((ulong)20);
+
+            // Verify all messages are intact.
+            for (ulong i = 1; i <= 20; i++)
+            {
+                var msg = await store.LoadAsync(i, default);
+                msg.ShouldNotBeNull();
+                var expected = Encoding.UTF8.GetBytes($"msg-{(int)(i - 1):D4}");
+                msg!.Payload.ToArray().ShouldBe(expected);
+            }
+        }
+    }
+
+    // Go: filestore.go purge — all blocks removed, fresh block created.
+    [Fact]
+    public async Task Purge_CleansAllBlocks()
+    {
+        var subDir = "blk-purge";
+        var dir = Path.Combine(_dir, subDir);
+
+        await using var store = CreateStore(subDir, new FileStoreOptions { BlockSizeBytes = 256 });
+
+        for (var i = 0; i < 20; i++)
+            await store.AppendAsync("foo", "Hello"u8.ToArray(), default);
+
+        // Before purge, multiple .blk files should exist.
+        Directory.GetFiles(dir, "*.blk").Length.ShouldBeGreaterThan(0);
+
+        await store.PurgeAsync(default);
+
+        var state = await store.GetStateAsync(default);
+        state.Messages.ShouldBe((ulong)0);
+        state.Bytes.ShouldBe((ulong)0);
+
+        // After purge, no old .blk files should remain (or they should be empty/recreated).
+        // The old JSONL file should also not exist.
+        File.Exists(Path.Combine(dir, "messages.jsonl")).ShouldBeFalse();
+    }
+
+    // Go: filestore.go dmap — soft-delete within a block.
+    [Fact]
+    public async Task Remove_SoftDeletesInBlock()
+    {
+        await using var store = CreateStore("blk-remove");
+
+        for (var i = 0; i < 5; i++)
+            await store.AppendAsync("foo", "data"u8.ToArray(), default);
+
+        // Remove sequence 3.
+        (await store.RemoveAsync(3, default)).ShouldBeTrue();
+
+        // Verify seq 3 returns null.
+        (await store.LoadAsync(3, default)).ShouldBeNull();
+
+        // Other sequences still loadable.
+        (await store.LoadAsync(1, default)).ShouldNotBeNull();
+        (await store.LoadAsync(2, default)).ShouldNotBeNull();
+        (await store.LoadAsync(4, default)).ShouldNotBeNull();
+        (await store.LoadAsync(5, default)).ShouldNotBeNull();
+
+        // State reflects the removal.
+        var state = await store.GetStateAsync(default);
+        state.Messages.ShouldBe((ulong)4);
+    }
+
+    // Go: filestore.go snapshot — iterates all blocks for snapshot creation.
+    [Fact]
+    public async Task Snapshot_IncludesAllBlocks()
+    {
+        await using var srcStore = CreateStore("blk-snap-src", new FileStoreOptions { BlockSizeBytes = 256 });
+
+        for (var i = 0; i < 30; i++)
+            await srcStore.AppendAsync("foo", Encoding.UTF8.GetBytes($"msg-{i}"), default);
+
+        // Verify multiple blocks.
+        srcStore.BlockCount.ShouldBeGreaterThan(1);
+
+        var snap = await srcStore.CreateSnapshotAsync(default);
+        snap.Length.ShouldBeGreaterThan(0);
+
+        // Restore into a new store.
+        await using var dstStore = CreateStore("blk-snap-dst");
+        await dstStore.RestoreSnapshotAsync(snap, default);
+
+        var srcState = await srcStore.GetStateAsync(default);
+        var dstState = await dstStore.GetStateAsync(default);
+        dstState.Messages.ShouldBe(srcState.Messages);
+        dstState.FirstSeq.ShouldBe(srcState.FirstSeq);
+        dstState.LastSeq.ShouldBe(srcState.LastSeq);
+
+        // Verify each message round-trips.
+        for (ulong i = 1; i <= srcState.Messages; i++)
+        {
+            var original = await srcStore.LoadAsync(i, default);
+            var copy = await dstStore.LoadAsync(i, default);
+            copy.ShouldNotBeNull();
+            copy!.Subject.ShouldBe(original!.Subject);
+            copy.Payload.ToArray().ShouldBe(original.Payload.ToArray());
+        }
+    }
+
+    // Go: filestore.go S2 compression — payload is compressed before block write.
+    [Fact]
+    public async Task Compression_RoundTrip()
+    {
+        var subDir = "blk-compress";
+
+        await using var store = CreateStore(subDir, new FileStoreOptions
+        {
+            Compression = StoreCompression.S2Compression,
+        });
+
+        var payload = "Hello, S2 compressed block storage!"u8.ToArray();
+        for (var i = 0; i < 10; i++)
+            await store.AppendAsync("foo", payload, default);
+
+        var state = await store.GetStateAsync(default);
+        state.Messages.ShouldBe((ulong)10);
+
+        // Verify all messages are readable with correct payload.
+        for (ulong i = 1; i <= 10; i++)
+        {
+            var msg = await store.LoadAsync(i, default);
+            msg.ShouldNotBeNull();
+            msg!.Payload.ToArray().ShouldBe(payload);
+        }
+    }
+
+    // Go: filestore.go AEAD encryption — payload is encrypted before block write.
+    [Fact]
+    public async Task Encryption_RoundTrip()
+    {
+        var subDir = "blk-encrypt";
+        var key = "nats-v2-test-key-exactly-32-bytes"u8[..32].ToArray();
+
+        await using var store = CreateStore(subDir, new FileStoreOptions
+        {
+            Cipher = StoreCipher.ChaCha,
+            EncryptionKey = key,
+        });
+
+        var payload = "Hello, AEAD encrypted block storage!"u8.ToArray();
+        for (var i = 0; i < 10; i++)
+            await store.AppendAsync("foo", payload, default);
+
+        var state = await store.GetStateAsync(default);
+        state.Messages.ShouldBe((ulong)10);
+
+        // Verify all messages are readable with correct payload.
+        for (ulong i = 1; i <= 10; i++)
+        {
+            var msg = await store.LoadAsync(i, default);
+            msg.ShouldNotBeNull();
+            msg!.Payload.ToArray().ShouldBe(payload);
+        }
+    }
+}