diff --git a/lib/entry-points.js b/lib/entry-points.js
index 8768a09aa..f6b126c84 100644
--- a/lib/entry-points.js
+++ b/lib/entry-points.js
@@ -145838,7 +145838,10 @@ function cacheCommandOutput(key, cmd, output) {
 function getCachedCommandOutput(key, cmd) {
   const memoized = inMemoryCache.get(key);
   if (memoized !== void 0) {
-    return memoized.output;
+    if (cmd === void 0 || memoized.cmd === cmd) {
+      return memoized.output;
+    }
+    inMemoryCache.delete(key);
   }
   const entry = readCommandCacheFile()[key];
   if (!isObject(entry) || !isString(entry.cmd) || cmd !== void 0 && entry.cmd !== cmd || !commandCacheValidators[key](entry.output)) {
diff --git a/src/cli/output-cache.test.ts b/src/cli/output-cache.test.ts
index c66af1491..e88e798cf 100644
--- a/src/cli/output-cache.test.ts
+++ b/src/cli/output-cache.test.ts
@@ -160,6 +160,21 @@ test.serial("cacheCommandOutput persists the output to the memo", async (t) => {
   });
 });
 
+test.serial(
+  "getCachedCommandOutput treats a memoized output from another CLI as a miss",
+  async (t) => {
+    await withCacheDir(() => {
+      cacheCommandOutput(CommandCacheKey.Version, "/path/to/other-codeql", {
+        version: "2.20.0",
+      });
+      t.is(
+        getCachedCommandOutput(CommandCacheKey.Version, "/path/to/codeql"),
+        undefined,
+      );
+    });
+  },
+);
+
 test.serial(
   "getCachedCommandOutput prefers the in-memory memo over the file",
   async (t) => {
@@ -181,3 +196,25 @@ test.serial(
     });
   },
 );
+
+test.serial(
+  "getCachedCommandOutput falls back to file when memoized output comes from another CLI",
+  async (t) => {
+    await withCacheDir((cacheFilePath) => {
+      cacheCommandOutput(CommandCacheKey.Version, "/path/to/other-codeql", {
+        version: "2.19.0",
+      });
+      writeCacheFile(cacheFilePath, {
+        [CommandCacheKey.Version]: {
+          cmd: "/path/to/codeql",
+          output: { version: "2.20.0", overlayVersion: 1 },
+        },
+      });
+
+      t.deepEqual(
+        getCachedCommandOutput(CommandCacheKey.Version, "/path/to/codeql"),
+        { version: "2.20.0", overlayVersion: 1 },
+      );
+    });
+  },
+);
diff --git a/src/cli/output-cache.ts b/src/cli/output-cache.ts
index 144e27fd1..dd7685148 100644
--- a/src/cli/output-cache.ts
+++ b/src/cli/output-cache.ts
@@ -195,7 +195,12 @@ export function getCachedCommandOutput<K extends CommandCacheKey>(
   // Tier 1: the in-memory variable.
   const memoized = inMemoryCache.get(key);
   if (memoized !== undefined) {
-    return memoized.output as CommandCacheKeyOutputMap[K];
+    if (cmd === undefined || memoized.cmd === cmd) {
+      return memoized.output as CommandCacheKeyOutputMap[K];
+    }
+    // If the memoized entry doesn't match the requested CLI,
+    // treat it as a miss and fall back to tier 2, the file.
+    inMemoryCache.delete(key);
   }
 
   // Tier 2: the temporary file persisted by an earlier step, if any.