diff --git a/src/gateway/session-compaction-checkpoints.test.ts b/src/gateway/session-compaction-checkpoints.test.ts
index 7271b1c7fb1..bba73ffed64 100644
--- a/src/gateway/session-compaction-checkpoints.test.ts
+++ b/src/gateway/session-compaction-checkpoints.test.ts
@@ -79,6 +79,8 @@ describe("session-compaction-checkpoints", () => {
 
       expect(sessionManagerOpenSpy).not.toHaveBeenCalled();
       expect(snapshot).not.toBeNull();
+      expect(snapshot?.agentId).toBe(DEFAULT_AGENT_ID);
+      expect(snapshot?.sourceSessionId).toBe(session.getSessionId());
       expect(snapshot?.leafId).toBe(leafId);
       expect(snapshot?.sessionFile).not.toBe(sessionFile);
       expect(snapshot?.sessionFile).toContain("sqlite-transcript://");
@@ -119,7 +121,14 @@ describe("session-compaction-checkpoints", () => {
           agentId: DEFAULT_AGENT_ID,
           sessionId: snapshot!.sessionId,
         }),
-      ).toBe(true);
+      ).toBe(false);
+      expect(
+        hasSqliteSessionTranscriptSnapshot({
+          agentId: DEFAULT_AGENT_ID,
+          sessionId: session.getSessionId(),
+          snapshotId: snapshot!.sessionId,
+        }),
+      ).toBe(false);
     } finally {
       sessionManagerOpenSpy.mockRestore();
     }
@@ -161,6 +170,8 @@ describe("session-compaction-checkpoints", () => {
 
       expect(sessionManagerOpenSpy).not.toHaveBeenCalled();
       expect(snapshot).not.toBeNull();
+      expect(snapshot?.agentId).toBe(DEFAULT_AGENT_ID);
+      expect(snapshot?.sourceSessionId).toBe(sessionId);
       expect(snapshot?.sessionId).not.toBe(sessionId);
       expect(snapshot?.leafId).toBe(leafId);
       expect(snapshot?.sessionFile).not.toBe(sessionFile);
diff --git a/src/gateway/session-compaction-checkpoints.ts b/src/gateway/session-compaction-checkpoints.ts
index ab481077aef..267a2ec4911 100644
--- a/src/gateway/session-compaction-checkpoints.ts
+++ b/src/gateway/session-compaction-checkpoints.ts
@@ -31,6 +31,8 @@ const MAX_COMPACTION_CHECKPOINTS_PER_SESSION = 25;
 export const MAX_COMPACTION_CHECKPOINT_SNAPSHOT_BYTES = 64 * 1024 * 1024;
 
 export type CapturedCompactionCheckpointSnapshot = {
+  agentId: string;
+  sourceSessionId: string;
   sessionId: string;
   sessionFile?: string;
   leafId: string;
@@ -289,6 +291,8 @@ export async function captureCompactionCheckpointSnapshotAsync(params: {
     },
   });
   return {
+    agentId: snapshotAgentId,
+    sourceSessionId: sourceHeader.id,
     sessionId: snapshotSessionId,
     sessionFile: snapshotFile,
     leafId,
@@ -298,7 +302,18 @@ export async function captureCompactionCheckpointSnapshotAsync(params: {
 export async function cleanupCompactionCheckpointSnapshot(
   snapshot: CapturedCompactionCheckpointSnapshot | null | undefined,
 ): Promise<void> {
-  void snapshot;
+  if (!snapshot) {
+    return;
+  }
+  deleteSqliteSessionTranscriptSnapshot({
+    agentId: snapshot.agentId,
+    sessionId: snapshot.sourceSessionId,
+    snapshotId: snapshot.sessionId,
+  });
+  deleteSqliteSessionTranscript({
+    agentId: snapshot.agentId,
+    sessionId: snapshot.sessionId,
+  });
 }
 
 export async function persistSessionCompactionCheckpoint(params: {