diff --git a/yarn-project/bb-prover/src/prover/bb_native_private_kernel_prover.ts b/yarn-project/bb-prover/src/prover/bb_native_private_kernel_prover.ts
index 87f9978db987..8fc119f52525 100644
--- a/yarn-project/bb-prover/src/prover/bb_native_private_kernel_prover.ts
+++ b/yarn-project/bb-prover/src/prover/bb_native_private_kernel_prover.ts
@@ -113,6 +113,7 @@ export class BBNativePrivateKernelProver extends BBPrivateKernelProver {
           throw err;
         }),
       this.skipCleanup,
+      this.log,
     );
   }
 }
diff --git a/yarn-project/bb-prover/src/prover/bb_prover.ts b/yarn-project/bb-prover/src/prover/bb_prover.ts
index 5075ccf5d382..c2131d4d0210 100644
--- a/yarn-project/bb-prover/src/prover/bb_prover.ts
+++ b/yarn-project/bb-prover/src/prover/bb_prover.ts
@@ -781,6 +781,7 @@ export class BBNativeRollupProver implements ServerCircuitProver {
           throw err;
         }),
       this.config.bbSkipCleanup,
+      logger,
     );
   }
 }
diff --git a/yarn-project/bb-prover/src/verifier/bb_verifier.ts b/yarn-project/bb-prover/src/verifier/bb_verifier.ts
index 7ef1312c9809..290db387a0c1 100644
--- a/yarn-project/bb-prover/src/verifier/bb_verifier.ts
+++ b/yarn-project/bb-prover/src/verifier/bb_verifier.ts
@@ -63,7 +63,7 @@ export class BBCircuitVerifier implements ClientProtocolCircuitVerifier {
         proofType: 'ultra-honk',
       } satisfies CircuitVerificationStats);
     };
-    await runInDirectory(this.config.bbWorkingDirectory, operation, this.config.bbSkipCleanup);
+    await runInDirectory(this.config.bbWorkingDirectory, operation, this.config.bbSkipCleanup, this.logger);
   }
 
   public async verifyProof(tx: Tx): Promise<boolean> {
@@ -103,7 +103,7 @@ export class BBCircuitVerifier implements ClientProtocolCircuitVerifier {
           proofType: 'client-ivc',
         } satisfies CircuitVerificationStats);
       };
-      await runInDirectory(this.config.bbWorkingDirectory, operation, this.config.bbSkipCleanup);
+      await runInDirectory(this.config.bbWorkingDirectory, operation, this.config.bbSkipCleanup, this.logger);
       return true;
     } catch (err) {
       this.logger.warn(`Failed to verify ClientIVC proof for tx ${Tx.getHash(tx)}: ${String(err)}`);
diff --git a/yarn-project/foundation/src/fs/run_in_dir.ts b/yarn-project/foundation/src/fs/run_in_dir.ts
index 2eb4d6f02552..714ec120da6e 100644
--- a/yarn-project/foundation/src/fs/run_in_dir.ts
+++ b/yarn-project/foundation/src/fs/run_in_dir.ts
@@ -1,12 +1,15 @@
 import { promises as fs } from 'fs';
 import * as path from 'path';
 
+import { createLogger } from '../log/pino-logger.js';
+
 // Create a random directory underneath a 'base' directory
 // Calls a provided method, ensures the random directory is cleaned up afterwards unless the operation fails
 export async function runInDirectory<T>(
   workingDirBase: string,
   fn: (dir: string) => Promise<T>,
   skipCleanup: boolean | undefined,
+  logger = createLogger('foundation:run-in-directory'),
 ): Promise<T> {
   // Create random directory to be used for temp files
   const workingDirectory = await fs.mkdtemp(path.join(workingDirBase, 'tmp-'));
@@ -22,8 +25,8 @@ export async function runInDirectory<T>(
     if (!skipCleanup) {
       try {
         await fs.rm(workingDirectory, { recursive: true, force: true, maxRetries: 3, retryDelay: 100 });
-      } catch {
-        // ignore cleanup errors
+      } catch (err) {
+        logger.warn(`Failed to cleanup temporary directory ${workingDirectory}: ${err}`, { err });
       }
     }
   }
diff --git a/yarn-project/simulator/src/providers/acvm_native.ts b/yarn-project/simulator/src/providers/acvm_native.ts
index 699318e99a81..69e7ef4d2c2b 100644
--- a/yarn-project/simulator/src/providers/acvm_native.ts
+++ b/yarn-project/simulator/src/providers/acvm_native.ts
@@ -158,7 +158,7 @@ export class NativeACVMSimulator implements SimulationProvider {
       return result.witness;
     };
 
-    return await runInDirectory(this.workingDirectory, operation, false);
+    return await runInDirectory(this.workingDirectory, operation, false, logger);
   }
 
   executeUserCircuit(