diff --git a/packages/angular/build/src/builders/unit-test/runners/vitest/plugins.ts b/packages/angular/build/src/builders/unit-test/runners/vitest/plugins.ts
index bd8a6926bfd6..d36f8a05ffa6 100644
--- a/packages/angular/build/src/builders/unit-test/runners/vitest/plugins.ts
+++ b/packages/angular/build/src/builders/unit-test/runners/vitest/plugins.ts
@@ -82,6 +82,18 @@ export async function createVitestConfigPlugin(
     async config(config) {
       const testConfig = config.test;
 
+      if (reporters !== undefined) {
+        delete testConfig?.reporters;
+      }
+
+      if (
+        options.coverage.reporters !== undefined &&
+        testConfig?.coverage &&
+        'reporter' in testConfig.coverage
+      ) {
+        delete testConfig.coverage.reporter;
+      }
+
       if (testConfig?.projects?.length) {
         this.warn(
           'The "test.projects" option in the Vitest configuration file is not supported. ' +
@@ -106,6 +118,14 @@ export async function createVitestConfigPlugin(
         delete testConfig.watch;
       }
 
+      if (testConfig?.exclude) {
+        this.warn(
+          'The "test.exclude" option in the Vitest configuration file is evaluated after ' +
+            'tests are compiled. For better build performance, please use the Angular CLI ' +
+            '"exclude" option instead.',
+        );
+      }
+
       // Merge user-defined plugins from the Vitest config with the CLI's internal plugins.
       if (config.plugins) {
         const userPlugins = config.plugins.filter(
@@ -398,6 +418,9 @@ async function generateCoverageOption(
   projectName: string,
 ): Promise<VitestCoverageOption> {
   let defaultExcludes: string[] = [];
+  // When a coverage exclude option is provided, Vitest's default coverage excludes
+  // will be overridden. To retain them, we manually fetch the defaults to append to the
+  // user's provided exclusions.
   if (optionsCoverage.exclude) {
     try {
       const vitestConfig = await import('vitest/config');
@@ -429,12 +452,15 @@ async function generateCoverageOption(
     // Special handling for `exclude`/`reporters` due to an undefined value causing upstream failures
     ...(optionsCoverage.exclude
       ? {
-          exclude: [
-            // Augment the default exclude https://vitest.dev/config/#coverage-exclude
-            // with the user defined exclusions
-            ...optionsCoverage.exclude,
-            ...defaultExcludes,
-          ],
+          exclude: Array.from(
+            new Set([
+              // Augment the default exclude https://vitest.dev/config/#coverage-exclude
+              // with the user defined exclusions
+              ...(configCoverage?.exclude || []),
+              ...optionsCoverage.exclude,
+              ...defaultExcludes,
+            ]),
+          ),
         }
       : {}),
     ...(optionsCoverage.reporters
diff --git a/packages/angular/build/src/builders/unit-test/tests/behavior/runner-config-vitest_spec.ts b/packages/angular/build/src/builders/unit-test/tests/behavior/runner-config-vitest_spec.ts
index fcfa3644035f..609d736e00f7 100644
--- a/packages/angular/build/src/builders/unit-test/tests/behavior/runner-config-vitest_spec.ts
+++ b/packages/angular/build/src/builders/unit-test/tests/behavior/runner-config-vitest_spec.ts
@@ -42,6 +42,21 @@ describeBuilder(execute, UNIT_TEST_BUILDER_INFO, (harness) => {
       harness.expectFile('vitest-results.xml').toExist();
     });
 
+    it('should override reporters defined in runnerConfig file when CLI option is present', async () => {
+      harness.useTarget('test', {
+        ...BASE_OPTIONS,
+        runnerConfig: 'vitest.config.ts',
+        reporters: ['default'],
+      });
+
+      harness.writeFile('vitest.config.ts', VITEST_CONFIG_CONTENT);
+
+      const { result } = await harness.executeOnce();
+      expect(result?.success).toBeTrue();
+      // The CLI option 'default' should override the 'junit' reporter in VITEST_CONFIG_CONTENT
+      harness.expectFile('vitest-results.xml').toNotExist();
+    });
+
     it('should use custom reportsDirectory defined in runnerConfig file', async () => {
       harness.useTarget('test', {
         ...BASE_OPTIONS,
@@ -164,6 +179,59 @@ describeBuilder(execute, UNIT_TEST_BUILDER_INFO, (harness) => {
       expect(results.numPassedTests).toBe(1);
     });
 
+    it('should correctly merge coverage.exclude arrays from builder and runner options', async () => {
+      harness.useTarget('test', {
+        ...BASE_OPTIONS,
+        coverage: true,
+        runnerConfig: 'vitest.config.ts',
+        coverageExclude: ['src/app/cli-excluded.ts'],
+      });
+
+      harness.writeFile(
+        'vitest.config.ts',
+        `
+        import { defineConfig } from 'vitest/config';
+        export default defineConfig({
+          test: {
+            coverage: {
+              exclude: ['src/app/config-excluded.ts'],
+            },
+          },
+        });
+        `,
+      );
+
+      // Create two files that would normally be covered
+      harness.writeFile('src/app/cli-excluded.ts', 'export const cliExcluded = true;');
+      harness.writeFile('src/app/config-excluded.ts', 'export const configExcluded = true;');
+
+      // Update the test file to import them so they're picked up by coverage
+      harness.writeFile(
+        'src/app/app.component.spec.ts',
+        `
+        import { test, expect } from 'vitest';
+        import './cli-excluded';
+        import './config-excluded';
+        test('should pass', () => {
+          expect(true).toBe(true);
+        });
+        `,
+      );
+
+      const { result } = await harness.executeOnce();
+      expect(result?.success).toBeTrue();
+      harness.expectFile('coverage/test/coverage-final.json').toExist();
+
+      const coverageMap = JSON.parse(harness.readFile('coverage/test/coverage-final.json'));
+      const coveredFiles = Object.keys(coverageMap);
+
+      const hasCliExcluded = coveredFiles.some((f) => f.includes('cli-excluded.ts'));
+      const hasConfigExcluded = coveredFiles.some((f) => f.includes('config-excluded.ts'));
+
+      expect(hasCliExcluded).withContext('CLI target should be excluded').toBeFalse();
+      expect(hasConfigExcluded).withContext('Config file target should be excluded').toBeFalse();
+    });
+
     it('should allow overriding globals to false via runnerConfig file', async () => {
       harness.useTarget('test', {
         ...BASE_OPTIONS,
@@ -348,6 +416,38 @@ describeBuilder(execute, UNIT_TEST_BUILDER_INFO, (harness) => {
       // );
     });
 
+    it('should warn about performance when "test.exclude" option is in runnerConfig file', async () => {
+      harness.useTarget('test', {
+        ...BASE_OPTIONS,
+        runnerConfig: 'vitest.config.ts',
+      });
+
+      harness.writeFile(
+        'vitest.config.ts',
+        `
+        import { defineConfig } from 'vitest/config';
+        export default defineConfig({
+          test: {
+            exclude: ['src/app/non-existent.spec.ts'],
+          },
+        });
+        `,
+      );
+
+      const { result, logs } = await harness.executeOnce();
+      expect(result?.success).toBeTrue();
+
+      // TODO: Re-enable once Vite logs are remapped through build system
+      // expect(logs).toContain(
+      //   jasmine.objectContaining({
+      //     level: 'warn',
+      //     message: jasmine.stringMatching(
+      //       'The "test.exclude" option in the Vitest configuration file is evaluated after',
+      //     ),
+      //   }),
+      // );
+    });
+
     it(`should append "test.setupFiles" (string) from runnerConfig to the CLI's setup`, async () => {
       harness.useTarget('test', {
         ...BASE_OPTIONS,