diff --git a/test/coverage-test/fixtures/configs/vitest.config.configure-vitest-hook.ts b/test/coverage-test/fixtures/configs/vitest.config.configure-vitest-hook.ts
new file mode 100644
index 000000000..2bcd70e6d
--- /dev/null
+++ b/test/coverage-test/fixtures/configs/vitest.config.configure-vitest-hook.ts
@@ -0,0 +1,18 @@
+import assert from 'node:assert';
+import { defineConfig } from 'vitest/config'
+
+export default defineConfig({
+  plugins: [{
+    name: "coverage-options-by-runtime-plugin",
+    configureVitest(context) {
+      const coverage = context.vitest.config.coverage
+      assert(coverage.provider === "v8" || coverage.provider === "istanbul")
+
+      coverage.include ||= []
+      coverage.include.push("**/even.ts");
+      coverage.include.push("**/untested-file.ts");
+
+      coverage.exclude.push("**/math.ts");
+    },
+  }],
+})
diff --git a/test/coverage-test/test/include-exclude.test.ts b/test/coverage-test/test/include-exclude.test.ts
index e8f3b3f52..51fba2c0f 100644
--- a/test/coverage-test/test/include-exclude.test.ts
+++ b/test/coverage-test/test/include-exclude.test.ts
@@ -1,3 +1,4 @@
+import assert from 'node:assert'
 import { expect } from 'vitest'
 import { coverageConfigDefaults } from 'vitest/config'
 import { readCoverageMap, runVitest, test } from '../utils'
@@ -59,3 +60,82 @@ test('test files are automatically excluded from report when excludes is set', a
   const files = coverageMap.files()
   expect(files.find(file => file.includes('test-that-looks-like-source-file'))).toBeFalsy()
 })
+
+test('files included and excluded in plugin\'s configureVitest are excluded', async () => {
+  await runVitest({
+    config: 'fixtures/configs/vitest.config.configure-vitest-hook.ts',
+    include: ['fixtures/test/math.test.ts', 'fixtures/test/even.test.ts'],
+    coverage: {
+      // Include math.ts by default, exclude it in plugin config
+      include: ['**/math.ts'],
+      all: true,
+      reporter: 'json',
+    },
+  })
+
+  const coverageMap = await readCoverageMap()
+  const files = coverageMap.files()
+
+  expect(files).toMatchInlineSnapshot(`
+    [
+      "<process-cwd>/fixtures/src/even.ts",
+      "<process-cwd>/fixtures/src/untested-file.ts",
+    ]
+  `)
+})
+
+test('files included and excluded in project\'s plugin\'s configureVitest are excluded', async () => {
+  await runVitest({
+    coverage: {
+      // Include math.ts by default, exclude it in plugin config
+      include: ['**/math.ts'],
+      all: true,
+      reporter: 'json',
+    },
+    projects: [
+      {
+        test: {
+          name: 'first',
+          include: ['fixtures/test/math.test.ts'],
+        },
+        plugins: [{
+          name: 'coverage-options-by-runtime-plugin',
+          configureVitest(context) {
+            const coverage = context.vitest.config.coverage
+            assert(coverage.provider === 'v8' || coverage.provider === 'istanbul')
+
+            coverage.include ||= []
+            coverage.include.push('**/even.ts')
+          },
+        }],
+      },
+      {
+        test: {
+          name: 'second',
+          include: ['fixtures/test/even.test.ts'],
+        },
+        plugins: [{
+          name: 'coverage-options-by-runtime-plugin',
+          configureVitest(context) {
+            const coverage = context.vitest.config.coverage
+            assert(coverage.provider === 'v8' || coverage.provider === 'istanbul')
+
+            coverage.include ||= []
+            coverage.include.push('**/untested-file.ts')
+            coverage.exclude.push('**/math.ts')
+          },
+        }],
+      },
+    ],
+  })
+
+  const coverageMap = await readCoverageMap()
+  const files = coverageMap.files()
+
+  expect(files).toMatchInlineSnapshot(`
+    [
+      "<process-cwd>/fixtures/src/even.ts",
+      "<process-cwd>/fixtures/src/untested-file.ts",
+    ]
+  `)
+})