diff --git a/gitnexus/src/core/run-analyze.ts b/gitnexus/src/core/run-analyze.ts
index 5d2684ec2..4ccfc8ad7 100644
--- a/gitnexus/src/core/run-analyze.ts
+++ b/gitnexus/src/core/run-analyze.ts
@@ -354,7 +354,14 @@ export async function runFullAnalysis(
       pipelineResult,
     };
   } catch (err) {
-    // Ensure LadybugDB is closed even on error
+    // Ensure native resources are closed even on error to prevent
+    // C++ atexit destructor races during process.exit() (#38, #40).
+    try {
+      const { disposeEmbedder } = await import('./embeddings/embedder.js');
+      await disposeEmbedder();
+    } catch {
+      /* swallow */
+    }
     try {
       await closeLbug();
     } catch {