diff --git a/scripts/bootstrap-env.mjs b/scripts/bootstrap-env.mjs
index 2e0a0a059e..a3c1c6fbaa 100644
--- a/scripts/bootstrap-env.mjs
+++ b/scripts/bootstrap-env.mjs
@@ -35,7 +35,7 @@ const OPTIONAL_OAUTH_SECRETS = [
 
 // ── Resolve DATA_DIR (mirrors dataPaths.ts logic) ───────────────────────────
 function resolveDataDir(overridePath, env = process.env) {
-  if (overridePath) return resolve(overridePath);
+  if (overridePath?.trim()) return resolve(overridePath);
 
   const configured = env.DATA_DIR?.trim();
   if (configured) return resolve(configured);
diff --git a/tests/unit/bootstrap-env.test.mjs b/tests/unit/bootstrap-env.test.mjs
index e8d271fb53..6249c44ade 100644
--- a/tests/unit/bootstrap-env.test.mjs
+++ b/tests/unit/bootstrap-env.test.mjs
@@ -100,3 +100,14 @@ test("bootstrapEnv fails closed when existing database cannot be inspected", ()
     );
   });
 });
+
+test("bootstrapEnv ignores blank dataDirOverride values", () => {
+  withTempEnv(({ dataDir }) => {
+    fs.mkdirSync(dataDir, { recursive: true });
+    fs.writeFileSync(path.join(dataDir, ".env"), "JWT_SECRET=jwt-from-dot-env\n", "utf8");
+
+    const env = bootstrapEnv({ dataDirOverride: "   ", quiet: true });
+
+    assert.equal(env.JWT_SECRET, "jwt-from-dot-env");
+  });
+});