diff --git a/tools/modern-tests/babel.test.js b/tools/modern-tests/babel.test.js
index 376d0f13f2..9ca2966792 100644
--- a/tools/modern-tests/babel.test.js
+++ b/tools/modern-tests/babel.test.js
@@ -19,23 +19,41 @@ describe('Babel App Bundling /', () => {
     },
     customAssertions: {
       afterRun: async ({ result }) => {
+        await assertFileExtensionModuleRules(result.outputLines);
       },
       afterRunRebuildClient: async ({ allConsoleLogs }) => {
         // Check for HMR output as enabled by default
-        await waitForMeteorOutput(allConsoleLogs, /.*HMR.*Updated modules:*/);
+        await waitForMeteorOutput(allConsoleLogs, /.*HMR.*Updated modules:.*/);
       },
       afterRunProduction: async ({ result }) => {
+        await assertFileExtensionModuleRules(result.outputLines);
       },
       afterRunProductionRebuildClient: async ({ allConsoleLogs }) => {
         // Check for HMR to not be enabled in production-like mode
         await waitForMeteorOutput(allConsoleLogs, /.*HMR.*Updated modules:*/, { negate: true });
       },
       afterTest: async ({ result }) => {
+        await assertFileExtensionModuleRules(result.outputLines);
       },
       afterTestOnce: async ({ result }) => {
+        await assertFileExtensionModuleRules(result.outputLines);
       },
       afterBuild: async ({ result }) => {
+        await assertFileExtensionModuleRules(result.outputLines);
       },
     }
   }));
 });
+
+/**
+ * Helper function to assert that output contains expected file extension moduel rules
+ * @param {string[]} outputLines - Array of output lines to check
+ * @returns {Promise<void>}
+ */
+export async function assertFileExtensionModuleRules(outputLines) {
+  // Check for custom and residual rules
+  await waitForMeteorOutput(outputLines, '/\\.(js|jsx)$/');
+  await waitForMeteorOutput(outputLines, '/\\.(tsx|ts|mts|cts|mjs|cjs)$/');
+  await waitForMeteorOutput(outputLines, '/\\.(graphql|gql)$/');
+  await waitForMeteorOutput(outputLines, '/\\.(?:[mc]?js|jsx|[mc]?ts|tsx)$/i', { negate: true });
+}
diff --git a/tools/modern-tests/coffeescript.test.js b/tools/modern-tests/coffeescript.test.js
index 4c2dcfa972..1ba0172445 100644
--- a/tools/modern-tests/coffeescript.test.js
+++ b/tools/modern-tests/coffeescript.test.js
@@ -25,7 +25,7 @@ describe('CoffeeScript App Bundling /', () => {
       },
       afterRunRebuildClient: async ({ allConsoleLogs }) => {
         // Check for HMR output as enabled by default
-        await waitForMeteorOutput(allConsoleLogs, /.*HMR.*Updated modules:*/);
+        await waitForMeteorOutput(allConsoleLogs, /.*HMR.*Updated modules:.*/);
       },
       afterRunProduction: async ({ result }) => {
         await waitForCoffeescriptEnvs(result.outputLines);
diff --git a/tools/modern-tests/react.test.js b/tools/modern-tests/react.test.js
index b724e07f70..3bd09ccfbf 100644
--- a/tools/modern-tests/react.test.js
+++ b/tools/modern-tests/react.test.js
@@ -83,7 +83,7 @@ describe('React App Bundling /', () => {
       },
       afterRunRebuildClient: async ({ allConsoleLogs }) => {
         // Check for HMR output as enabled by default
-        await waitForMeteorOutput(allConsoleLogs, /.*HMR.*Updated modules:*/);
+        await waitForMeteorOutput(allConsoleLogs, /.*HMR.*Updated modules:.*/);
       },
       afterRunProduction: async ({ result }) => {
         await waitForReactEnvs(result.outputLines, { isJsxEnabled: true });
diff --git a/tools/modern-tests/typescript.test.js b/tools/modern-tests/typescript.test.js
index 67468f7860..c52fec5d94 100644
--- a/tools/modern-tests/typescript.test.js
+++ b/tools/modern-tests/typescript.test.js
@@ -24,7 +24,7 @@ describe('TypeScript App Bundling /', () => {
       },
       afterRunRebuildClient: async ({ allConsoleLogs }) => {
         // Check for HMR output as enabled by default
-        await waitForMeteorOutput(allConsoleLogs, /.*HMR.*Updated modules:*/);
+        await waitForMeteorOutput(allConsoleLogs, /.*HMR.*Updated modules:.*/);
       },
       afterRunProduction: async ({ result }) => {
         await waitForTypeScriptEnvs(result.outputLines, { isTsxEnabled: true });