diff --git a/pkg/memory/jsonl.go b/pkg/memory/jsonl.go
index 266f453d9..be71396ca 100644
--- a/pkg/memory/jsonl.go
+++ b/pkg/memory/jsonl.go
@@ -328,7 +328,74 @@ func (s *JSONLStore) SetHistory(
 	l.Lock()
 	defer l.Unlock()
 
-	// Rewrite the JSONL file atomically (temp + rename).
+	err := s.rewriteJSONL(sessionKey, history)
+	if err != nil {
+		return err
+	}
+
+	meta, err := s.readMeta(sessionKey)
+	if err != nil {
+		return err
+	}
+	now := time.Now()
+	if meta.CreatedAt.IsZero() {
+		meta.CreatedAt = now
+	}
+	meta.Skip = 0
+	meta.Count = len(history)
+	meta.UpdatedAt = now
+
+	return s.writeMeta(sessionKey, meta)
+}
+
+// Compact physically rewrites the JSONL file, dropping all logically
+// skipped lines. This reclaims disk space that accumulates after
+// repeated TruncateHistory calls.
+//
+// It is safe to call at any time; if there is nothing to compact
+// (skip == 0) the method returns immediately.
+func (s *JSONLStore) Compact(
+	_ context.Context, sessionKey string,
+) error {
+	l := s.sessionLock(sessionKey)
+	l.Lock()
+	defer l.Unlock()
+
+	meta, err := s.readMeta(sessionKey)
+	if err != nil {
+		return err
+	}
+	if meta.Skip == 0 {
+		return nil
+	}
+
+	all, err := readMessages(s.jsonlPath(sessionKey))
+	if err != nil {
+		return err
+	}
+
+	// Keep only the active (non-skipped) messages.
+	var active []providers.Message
+	if meta.Skip < len(all) {
+		active = all[meta.Skip:]
+	}
+
+	err = s.rewriteJSONL(sessionKey, active)
+	if err != nil {
+		return err
+	}
+
+	meta.Skip = 0
+	meta.Count = len(active)
+	meta.UpdatedAt = time.Now()
+
+	return s.writeMeta(sessionKey, meta)
+}
+
+// rewriteJSONL atomically replaces the JSONL file with the given messages.
+func (s *JSONLStore) rewriteJSONL(
+	sessionKey string, msgs []providers.Message,
+) error {
 	target := s.jsonlPath(sessionKey)
 	tmp := target + ".tmp"
 
@@ -337,7 +404,7 @@ func (s *JSONLStore) SetHistory(
 		return fmt.Errorf("memory: create jsonl tmp: %w", err)
 	}
 
-	for i, msg := range history {
+	for i, msg := range msgs {
 		line, marshalErr := json.Marshal(msg)
 		if marshalErr != nil {
 			f.Close()
@@ -364,21 +431,7 @@ func (s *JSONLStore) SetHistory(
 		_ = os.Remove(tmp)
 		return fmt.Errorf("memory: rename jsonl: %w", err)
 	}
-
-	// Reset metadata: skip=0, count=len(history).
-	meta, err := s.readMeta(sessionKey)
-	if err != nil {
-		return err
-	}
-	now := time.Now()
-	if meta.CreatedAt.IsZero() {
-		meta.CreatedAt = now
-	}
-	meta.Skip = 0
-	meta.Count = len(history)
-	meta.UpdatedAt = now
-
-	return s.writeMeta(sessionKey, meta)
+	return nil
 }
 
 func (s *JSONLStore) Close() error {
diff --git a/pkg/memory/jsonl_test.go b/pkg/memory/jsonl_test.go
index 57675504d..e3b53bfde 100644
--- a/pkg/memory/jsonl_test.go
+++ b/pkg/memory/jsonl_test.go
@@ -423,6 +423,127 @@ func TestColonInKey(t *testing.T) {
 	}
 }
 
+func TestCompact_RemovesSkippedMessages(t *testing.T) {
+	store := newTestStore(t)
+	ctx := context.Background()
+
+	// Write 10 messages, then truncate to keep last 3.
+	for i := 0; i < 10; i++ {
+		err := store.AddMessage(ctx, "compact", "user", string(rune('a'+i)))
+		if err != nil {
+			t.Fatalf("AddMessage: %v", err)
+		}
+	}
+	err := store.TruncateHistory(ctx, "compact", 3)
+	if err != nil {
+		t.Fatalf("TruncateHistory: %v", err)
+	}
+
+	// Before compact: file still has 10 lines.
+	allOnDisk, err := readMessages(store.jsonlPath("compact"))
+	if err != nil {
+		t.Fatalf("readMessages: %v", err)
+	}
+	if len(allOnDisk) != 10 {
+		t.Fatalf("before compact: expected 10 on disk, got %d", len(allOnDisk))
+	}
+
+	// Compact.
+	err = store.Compact(ctx, "compact")
+	if err != nil {
+		t.Fatalf("Compact: %v", err)
+	}
+
+	// After compact: file should have only 3 lines.
+	allOnDisk, err = readMessages(store.jsonlPath("compact"))
+	if err != nil {
+		t.Fatalf("readMessages: %v", err)
+	}
+	if len(allOnDisk) != 3 {
+		t.Fatalf("after compact: expected 3 on disk, got %d", len(allOnDisk))
+	}
+
+	// GetHistory should still return the same 3 messages.
+	history, err := store.GetHistory(ctx, "compact")
+	if err != nil {
+		t.Fatalf("GetHistory: %v", err)
+	}
+	if len(history) != 3 {
+		t.Fatalf("expected 3, got %d", len(history))
+	}
+	if history[0].Content != "h" || history[2].Content != "j" {
+		t.Errorf("wrong content: %+v", history)
+	}
+}
+
+func TestCompact_NoOpWhenNoSkip(t *testing.T) {
+	store := newTestStore(t)
+	ctx := context.Background()
+
+	for i := 0; i < 5; i++ {
+		err := store.AddMessage(ctx, "noop", "user", "msg")
+		if err != nil {
+			t.Fatalf("AddMessage: %v", err)
+		}
+	}
+
+	// Compact without prior truncation — should be a no-op.
+	err := store.Compact(ctx, "noop")
+	if err != nil {
+		t.Fatalf("Compact: %v", err)
+	}
+
+	history, err := store.GetHistory(ctx, "noop")
+	if err != nil {
+		t.Fatalf("GetHistory: %v", err)
+	}
+	if len(history) != 5 {
+		t.Errorf("expected 5, got %d", len(history))
+	}
+}
+
+func TestCompact_ThenAppend(t *testing.T) {
+	store := newTestStore(t)
+	ctx := context.Background()
+
+	for i := 0; i < 8; i++ {
+		err := store.AddMessage(ctx, "cap", "user", string(rune('a'+i)))
+		if err != nil {
+			t.Fatalf("AddMessage: %v", err)
+		}
+	}
+
+	err := store.TruncateHistory(ctx, "cap", 2)
+	if err != nil {
+		t.Fatalf("TruncateHistory: %v", err)
+	}
+	err = store.Compact(ctx, "cap")
+	if err != nil {
+		t.Fatalf("Compact: %v", err)
+	}
+
+	// Append after compaction should work correctly.
+	err = store.AddMessage(ctx, "cap", "user", "new")
+	if err != nil {
+		t.Fatalf("AddMessage after compact: %v", err)
+	}
+
+	history, err := store.GetHistory(ctx, "cap")
+	if err != nil {
+		t.Fatalf("GetHistory: %v", err)
+	}
+	if len(history) != 3 {
+		t.Fatalf("expected 3, got %d", len(history))
+	}
+	// g, h (kept from truncation), new (appended after compaction).
+	if history[0].Content != "g" {
+		t.Errorf("first = %q, want 'g'", history[0].Content)
+	}
+	if history[2].Content != "new" {
+		t.Errorf("last = %q, want 'new'", history[2].Content)
+	}
+}
+
 func TestCrashRecovery_PartialLine(t *testing.T) {
 	store := newTestStore(t)
 	ctx := context.Background()
diff --git a/pkg/memory/store.go b/pkg/memory/store.go
index 6887ec26e..b6e11707d 100644
--- a/pkg/memory/store.go
+++ b/pkg/memory/store.go
@@ -33,6 +33,10 @@ type Store interface {
 	// SetHistory replaces all messages in a session with the provided history.
 	SetHistory(ctx context.Context, sessionKey string, history []providers.Message) error
 
+	// Compact reclaims storage by physically removing logically truncated
+	// data. Backends that do not accumulate dead data may return nil.
+	Compact(ctx context.Context, sessionKey string) error
+
 	// Close releases any resources held by the store.
 	Close() error
 }