diff --git a/lib/entry-points.js b/lib/entry-points.js
index 07b48863f..e3ad62295 100644
--- a/lib/entry-points.js
+++ b/lib/entry-points.js
@@ -149934,9 +149934,12 @@ function readCommandCacheFile() {
   }
   return {};
 }
-function writeCommandCacheFile(data) {
+function writeCommandCacheFile() {
   try {
-    fs6.writeFileSync(getCommandCacheFilePath(), JSON.stringify(data));
+    fs6.writeFileSync(
+      getCommandCacheFilePath(),
+      JSON.stringify(Object.fromEntries(inMemoryCache))
+    );
   } catch (e) {
     logger.warning(`Failed to write command cache file: ${e}`);
   }
@@ -149944,9 +149947,6 @@ function writeCommandCacheFile(data) {
 function cacheCommandOutput(key, cmd, output) {
   const entry = { cmd, output };
   inMemoryCache.set(key, entry);
-  const data = readCommandCacheFile();
-  data[key] = entry;
-  writeCommandCacheFile(data);
 }
 function getCachedCommandOutput(key, cmd, validate) {
   const memoized = inMemoryCache.get(key);
@@ -159013,6 +159013,8 @@ async function run3(startedAt) {
     toolsVersion = initCodeQLResult.toolsVersion;
     toolsSource = initCodeQLResult.toolsSource;
     zstdAvailability = initCodeQLResult.zstdAvailability;
+    await codeql.getVersion();
+    await codeql.resolveLanguages();
     await checkWorkflow(logger2, codeql);
     if (
       // Only enable the experimental features env variable for Rust analysis if the user has explicitly
@@ -159322,6 +159324,7 @@ exec ${goBinaryPath} "$@"`
     await saveConfig(config, logger2);
     core20.setOutput("codeql-path", config.codeQLCmd);
     core20.setOutput("codeql-version", (await codeql.getVersion()).version);
+    writeCommandCacheFile();
   } catch (unwrappedError) {
     const error3 = wrapError(unwrappedError);
     core20.setFailed(error3.message);
diff --git a/src/cache.test.ts b/src/cache.test.ts
index c76e4719f..71a07b4c4 100644
--- a/src/cache.test.ts
+++ b/src/cache.test.ts
@@ -170,32 +170,19 @@ test.serial(
   },
 );
 
-test.serial(
-  "cacheCommandOutput persists the output to both the memo and the file",
-  async (t) => {
-    await withCacheDir((cacheFilePath) => {
-      cacheCommandOutput(CommandCacheKey.Version, "/path/to/codeql", {
-        hello: "world",
-      });
-
-      // Tier 2: the temporary file contains the entry.
-      const onDisk = JSON.parse(
-        fs.readFileSync(cacheFilePath, "utf8"),
-      ) as Record<string, unknown>;
-      t.deepEqual(onDisk[CommandCacheKey.Version], {
-        cmd: "/path/to/codeql",
-        output: { hello: "world" },
-      });
-
-      // Tier 1: the value is served from the memo even after the file is gone.
-      fs.rmSync(cacheFilePath);
-      t.deepEqual(
-        getCachedCommandOutput(CommandCacheKey.Version, "/path/to/codeql"),
-        { hello: "world" },
-      );
+test.serial("cacheCommandOutput persists the output to the memo", async (t) => {
+  await withCacheDir(() => {
+    cacheCommandOutput(CommandCacheKey.Version, "/path/to/codeql", {
+      hello: "world",
     });
-  },
-);
+
+    // Tier 1: the value is immediately available from the memo.
+    t.deepEqual(
+      getCachedCommandOutput(CommandCacheKey.Version, "/path/to/codeql"),
+      { hello: "world" },
+    );
+  });
+});
 
 test.serial(
   "getCachedCommandOutput prefers the in-memory memo over the file",
@@ -207,7 +194,10 @@ test.serial(
 
       // Overwrite the file with a different value; the memo (tier 1) should win.
       writeCacheFile(cacheFilePath, {
-        [CommandCacheKey.Version]: { cmd: "/path/to/codeql", output: { value: 2 } },
+        [CommandCacheKey.Version]: {
+          cmd: "/path/to/codeql",
+          output: { value: 2 },
+        },
       });
       t.deepEqual(
         getCachedCommandOutput(CommandCacheKey.Version, "/path/to/codeql"),
diff --git a/src/cache.ts b/src/cache.ts
index 660a0eb9c..32ec7f986 100644
--- a/src/cache.ts
+++ b/src/cache.ts
@@ -65,20 +65,22 @@ function readCommandCacheFile(): Record<string, CommandCacheEntry> {
 }
 
 /**
- * Persists the cache to the temporary file. Best-effort: a failure to write
+ * Persists the in-memory cache to the temporary file. Best-effort: a failure to write
  * just means a later step re-runs the CLI.
  */
-function writeCommandCacheFile(data: Record<string, CommandCacheEntry>): void {
+export function writeCommandCacheFile(): void {
   try {
-    fs.writeFileSync(getCommandCacheFilePath(), JSON.stringify(data));
+    fs.writeFileSync(
+      getCommandCacheFilePath(),
+      JSON.stringify(Object.fromEntries(inMemoryCache)),
+    );
   } catch (e) {
     logger.warning(`Failed to write command cache file: ${e}`);
   }
 }
 
 /**
- * Stores the output of a command under `key`, writing it to both the in-memory
- * memo (tier 1) and the temporary file (tier 2).
+ * Stores the output of a CLI command under `key` in a module-global object.
  */
 export function cacheCommandOutput(
   key: CommandCacheKey,
@@ -87,10 +89,6 @@ export function cacheCommandOutput(
 ): void {
   const entry: CommandCacheEntry = { cmd, output };
   inMemoryCache.set(key, entry);
-
-  const data = readCommandCacheFile();
-  data[key] = entry;
-  writeCommandCacheFile(data);
 }
 
 /**
diff --git a/src/init-action.ts b/src/init-action.ts
index 9c9b45556..dbcb2f054 100644
--- a/src/init-action.ts
+++ b/src/init-action.ts
@@ -19,6 +19,7 @@ import {
 } from "./actions-util";
 import { AnalysisKind, getAnalysisKinds } from "./analyses";
 import { getGitHubVersion, GitHubApiCombinedDetails } from "./api-client";
+import { writeCommandCacheFile } from "./cache";
 import {
   getDependencyCachingEnabled,
   getTotalCacheSize,
@@ -323,6 +324,11 @@ async function run(startedAt: Date) {
     toolsSource = initCodeQLResult.toolsSource;
     zstdAvailability = initCodeQLResult.zstdAvailability;
 
+    // Populate the in-memory command cache with CLI version and languages.
+    // These results will be persisted to disk at the end of the init action.
+    await codeql.getVersion();
+    await codeql.resolveLanguages();
+
     // Check the workflow for problems. If there are any problems, they are reported
     // to the workflow log. No exceptions are thrown.
     await checkWorkflow(logger, codeql);
@@ -766,6 +772,9 @@ async function run(startedAt: Date) {
 
     core.setOutput("codeql-path", config.codeQLCmd);
     core.setOutput("codeql-version", (await codeql.getVersion()).version);
+
+    // Persist the command cache to disk at the end of a successful init.
+    writeCommandCacheFile();
   } catch (unwrappedError) {
     const error = wrapError(unwrappedError);
     core.setFailed(error.message);