diff --git a/gitnexus/src/cli/analyze.ts b/gitnexus/src/cli/analyze.ts
index c77903de0..79f60b3fc 100644
--- a/gitnexus/src/cli/analyze.ts
+++ b/gitnexus/src/cli/analyze.ts
@@ -290,5 +290,7 @@ export const analyzeCommand = async (inputPath?: string, options?: AnalyzeOption
   // LadybugDB's native module holds open handles that prevent Node from exiting.
   // ONNX Runtime also registers native atexit hooks that segfault on some
   // platforms (#38, #40). Force-exit to ensure clean termination.
+  // The ONNX session is disposed in runFullAnalysis after embeddings complete
+  // to prevent C++ atexit destructors from racing with closed DB handles.
   process.exit(0);
 };
diff --git a/gitnexus/src/core/run-analyze.ts b/gitnexus/src/core/run-analyze.ts
index e8a108c71..5d2684ec2 100644
--- a/gitnexus/src/core/run-analyze.ts
+++ b/gitnexus/src/core/run-analyze.ts
@@ -265,6 +265,15 @@ export async function runFullAnalysis(
         {},
         cachedEmbeddingNodeIds.size > 0 ? cachedEmbeddingNodeIds : undefined,
       );
+
+      // Release ONNX Runtime session to prevent its C++ atexit handlers from
+      // racing with LadybugDB cleanup during process.exit() (#38, #40).
+      try {
+        const { disposeEmbedder } = await import('./embeddings/embedder.js');
+        await disposeEmbedder();
+      } catch {
+        /* best-effort */
+      }
     }
 
     // ── Phase 5: Finalize (98–100%) ───────────────────────────────────