diff --git a/e2e/test/coverage-analysis/jest-spec/jest.config.json b/e2e/test/coverage-analysis/jest-spec/jest.config.json
index 18679b42cc..7dc4da8390 100644
--- a/e2e/test/coverage-analysis/jest-spec/jest.config.json
+++ b/e2e/test/coverage-analysis/jest-spec/jest.config.json
@@ -1,4 +1,5 @@
 {
   "testEnvironment": "node",
-  "testMatch": ["**/jest-spec/*.spec.js"]
+  "rootDir": "..",
+  "testMatch": ["<rootDir>/jest-spec/*.spec.js"]
 }
diff --git a/packages/jest-runner/src/config-loaders/custom-jest-config-loader.ts b/packages/jest-runner/src/config-loaders/custom-jest-config-loader.ts
index 13bb2e7935..3b565304c8 100644
--- a/packages/jest-runner/src/config-loaders/custom-jest-config-loader.ts
+++ b/packages/jest-runner/src/config-loaders/custom-jest-config-loader.ts
@@ -51,7 +51,7 @@ export class CustomJestConfigLoader implements JestConfigLoader {
   private resolvePackageJsonFilePath(): string | undefined {
     const jestOptions = this.options as JestRunnerOptionsWithStrykerOptions;
     const packageJsonCandidate = path.resolve(jestOptions.jest.configFile ?? 'package.json');
-    if (packageJsonCandidate.endsWith('.json') && (jestOptions.jest.configFile || fs.existsSync(packageJsonCandidate))) {
+    if (packageJsonCandidate.endsWith('package.json') && (jestOptions.jest.configFile || fs.existsSync(packageJsonCandidate))) {
       return packageJsonCandidate;
     }
     return undefined;
@@ -63,7 +63,7 @@ export class CustomJestConfigLoader implements JestConfigLoader {
   private resolveJestConfigFilePath(): string | undefined {
     const jestOptions = this.options as JestRunnerOptionsWithStrykerOptions;
     const configFileCandidate = path.resolve(jestOptions.jest.configFile ?? 'jest.config.js');
-    if (configFileCandidate.endsWith('.js') && (jestOptions.jest.configFile || fs.existsSync(configFileCandidate))) {
+    if (!configFileCandidate.endsWith('package.json') && (jestOptions.jest.configFile || fs.existsSync(configFileCandidate))) {
       return configFileCandidate;
     }
     return undefined;
diff --git a/packages/jest-runner/src/jest-test-adapters/jest-greater-than-25-adapter.ts b/packages/jest-runner/src/jest-test-adapters/jest-greater-than-25-adapter.ts
index b3f493ed94..b4ea5a2f9b 100644
--- a/packages/jest-runner/src/jest-test-adapters/jest-greater-than-25-adapter.ts
+++ b/packages/jest-runner/src/jest-test-adapters/jest-greater-than-25-adapter.ts
@@ -4,7 +4,7 @@ import { JestRunResult } from '../jest-run-result';
 import { JestTestAdapter, RunSettings } from './jest-test-adapter';
 
 export class JestGreaterThan25TestAdapter implements JestTestAdapter {
-  public async run({ jestConfig, projectRoot, fileNameUnderTest, testNamePattern, testLocationInResults }: RunSettings): Promise<JestRunResult> {
+  public async run({ jestConfig, fileNameUnderTest, testNamePattern, testLocationInResults }: RunSettings): Promise<JestRunResult> {
     const config = JSON.stringify(jestConfig);
     const result = await jestWrapper.runCLI(
       {
@@ -17,7 +17,7 @@ export class JestGreaterThan25TestAdapter implements JestTestAdapter {
         testNamePattern,
         testLocationInResults,
       },
-      [projectRoot]
+      [jestConfig.rootDir ?? process.cwd()]
     );
     return result;
   }
diff --git a/packages/jest-runner/src/jest-test-adapters/jest-less-than-25-adapter.ts b/packages/jest-runner/src/jest-test-adapters/jest-less-than-25-adapter.ts
index 750eb5d1a1..9c792b35ec 100644
--- a/packages/jest-runner/src/jest-test-adapters/jest-less-than-25-adapter.ts
+++ b/packages/jest-runner/src/jest-test-adapters/jest-less-than-25-adapter.ts
@@ -1,5 +1,3 @@
-import { Config } from '@jest/types';
-
 import { jestWrapper } from '../utils';
 import { JestRunResult } from '../jest-run-result';
 
@@ -10,17 +8,20 @@ import { RunSettings, JestTestAdapter } from './jest-test-adapter';
  * It has a lot of `any` typings here, since the installed typings are not in sync.
  */
 export class JestLessThan25TestAdapter implements JestTestAdapter {
-  public run({ jestConfig, projectRoot, fileNameUnderTest, testNamePattern, testLocationInResults }: RunSettings): Promise<JestRunResult> {
+  public run({ jestConfig, fileNameUnderTest, testNamePattern, testLocationInResults }: RunSettings): Promise<JestRunResult> {
     const config = JSON.stringify(jestConfig);
     return jestWrapper.runCLI(
       {
-        ...(fileNameUnderTest && { _: [fileNameUnderTest], findRelatedTests: true }),
+        $0: 'stryker',
+        _: fileNameUnderTest ? [fileNameUnderTest] : [],
+        findRelatedTests: !!fileNameUnderTest,
         config,
         runInBand: true,
         silent: true,
         testNamePattern,
-      } as Config.Argv,
-      [projectRoot]
+        testLocationInResults,
+      },
+      [jestConfig.rootDir ?? process.cwd()]
     );
   }
 }
diff --git a/packages/jest-runner/src/jest-test-adapters/jest-test-adapter.ts b/packages/jest-runner/src/jest-test-adapters/jest-test-adapter.ts
index 67b3e5f29b..a67c560188 100644
--- a/packages/jest-runner/src/jest-test-adapters/jest-test-adapter.ts
+++ b/packages/jest-runner/src/jest-test-adapters/jest-test-adapter.ts
@@ -4,7 +4,6 @@ import { JestRunResult } from '../jest-run-result';
 
 export interface RunSettings {
   jestConfig: Config.InitialOptions;
-  projectRoot: string;
   testNamePattern?: string;
   fileNameUnderTest?: string;
   testLocationInResults?: boolean;
diff --git a/packages/jest-runner/src/jest-test-runner.ts b/packages/jest-runner/src/jest-test-runner.ts
index dead686c58..04e74f2853 100644
--- a/packages/jest-runner/src/jest-test-runner.ts
+++ b/packages/jest-runner/src/jest-test-runner.ts
@@ -106,7 +106,6 @@ export class JestTestRunner implements TestRunner {
     try {
       const { dryRunResult, jestResult } = await this.run({
         jestConfig: withCoverageAnalysis(this.jestConfig, coverageAnalysis),
-        projectRoot: process.cwd(),
         testLocationInResults: true,
       });
       if (dryRunResult.status === DryRunStatus.Complete && coverageAnalysis !== 'off') {
@@ -138,7 +137,6 @@ export class JestTestRunner implements TestRunner {
       const { dryRunResult } = await this.run({
         fileNameUnderTest,
         jestConfig: this.configForMutantRun(fileNameUnderTest),
-        projectRoot: process.cwd(),
         testNamePattern,
       });
       return toMutantRunResult(dryRunResult);
diff --git a/packages/jest-runner/src/plugin-tokens.ts b/packages/jest-runner/src/plugin-tokens.ts
index 777b8d7cf6..b9076cb61d 100644
--- a/packages/jest-runner/src/plugin-tokens.ts
+++ b/packages/jest-runner/src/plugin-tokens.ts
@@ -1,5 +1,3 @@
-export const projectRoot = 'projectRoot';
-export const loader = 'loader';
 export const resolve = 'resolve';
 export const configLoader = 'configLoader';
 export const processEnv = 'processEnv';
diff --git a/packages/jest-runner/src/utils/index.ts b/packages/jest-runner/src/utils/index.ts
index 762120faf9..1b68b5b767 100644
--- a/packages/jest-runner/src/utils/index.ts
+++ b/packages/jest-runner/src/utils/index.ts
@@ -1,4 +1,3 @@
-export * from './create-react-jest-config';
 export * from './verify-all-test-files-have-coverage';
 export * from './merge-mutant-coverage';
 export * from './jest-wrapper';
diff --git a/packages/jest-runner/test/integration/config-in-child-dir.it.spec.ts b/packages/jest-runner/test/integration/config-in-child-dir.it.spec.ts
new file mode 100644
index 0000000000..9835c32cb8
--- /dev/null
+++ b/packages/jest-runner/test/integration/config-in-child-dir.it.spec.ts
@@ -0,0 +1,27 @@
+import { commonTokens } from '@stryker-mutator/api/plugin';
+import { assertions, factory, testInjector } from '@stryker-mutator/test-helpers';
+import { expect } from 'chai';
+
+import { JestOptions } from '../../src-generated/jest-runner-options';
+import { JestRunnerOptionsWithStrykerOptions } from '../../src/jest-runner-options-with-stryker-options';
+import { jestTestRunnerFactory } from '../../src/jest-test-runner';
+import { createJestOptions } from '../helpers/producers';
+
+import { resolveTestResource } from '../helpers/resolve-test-resource';
+
+describe('jest with config in child dir', () => {
+  function createSut(overrides?: Partial<JestOptions>) {
+    const options: JestRunnerOptionsWithStrykerOptions = factory.strykerWithPluginOptions({
+      jest: createJestOptions(overrides),
+    });
+    return testInjector.injector.provideValue(commonTokens.options, options).injectFunction(jestTestRunnerFactory);
+  }
+
+  it('should still be able perform a mutant run', async () => {
+    process.chdir(resolveTestResource('config-in-child-dir'));
+    const sut = createSut({ configFile: 'client/jest.config.js' });
+    const actual = await sut.dryRun(factory.dryRunOptions());
+    assertions.expectCompleted(actual);
+    expect(actual.tests).lengthOf(2);
+  });
+});
diff --git a/packages/jest-runner/test/unit/config-loaders/custom-config-loader.spec.ts b/packages/jest-runner/test/unit/config-loaders/custom-config-loader.spec.ts
index 8c6df70ff4..fff1797c16 100644
--- a/packages/jest-runner/test/unit/config-loaders/custom-config-loader.spec.ts
+++ b/packages/jest-runner/test/unit/config-loaders/custom-config-loader.spec.ts
@@ -57,6 +57,19 @@ describe(CustomJestConfigLoader.name, () => {
     expect(config).to.deep.contains({ rootDir: path.resolve(projectRoot, 'lib') });
   });
 
+  it('should allow users to configure a jest.config.json file as "configFile"', () => {
+    // Arrange
+    fileExistsSyncStub.returns(true);
+    options.jest.configFile = path.resolve(projectRoot, 'jest.config.json');
+
+    // Act
+    const config = sut.loadConfig();
+
+    // Assert
+    expect(requireStub).calledWith(path.join(projectRoot, 'jest.config.json'));
+    expect(config).to.deep.contain(readConfig);
+  });
+
   it('should allow users to configure a package.json file as "configFile"', () => {
     // Arrange
     fileExistsSyncStub
diff --git a/packages/jest-runner/test/unit/jest-test-adapters/jest-greater-than-25-adapter.spec.ts b/packages/jest-runner/test/unit/jest-test-adapters/jest-greater-than-25-adapter.spec.ts
index dfc892ceab..78b106bbbf 100644
--- a/packages/jest-runner/test/unit/jest-test-adapters/jest-greater-than-25-adapter.spec.ts
+++ b/packages/jest-runner/test/unit/jest-test-adapters/jest-greater-than-25-adapter.spec.ts
@@ -11,11 +11,11 @@ describe(JestGreaterThan25TestAdapter.name, () => {
   let sut: JestGreaterThan25TestAdapter;
   let runCLIStub: sinon.SinonStub;
 
-  const projectRoot = '/path/to/project';
   const fileNameUnderTest = '/path/to/file';
-  const jestConfig: Config.InitialOptions = { rootDir: projectRoot };
+  let jestConfig: Config.InitialOptions;
 
   beforeEach(() => {
+    jestConfig = { rootDir: '/path/to/project' };
     runCLIStub = sinon.stub(jestWrapper, 'runCLI');
     runCLIStub.resolves({
       config: jestConfig,
@@ -25,63 +25,69 @@ describe(JestGreaterThan25TestAdapter.name, () => {
     sut = testInjector.injector.injectClass(JestGreaterThan25TestAdapter);
   });
 
-  it('should call the runCLI method with the correct ---projectRoot', async () => {
-    await sut.run({ jestConfig, projectRoot });
-    expect(runCLIStub).calledWith(sinon.match.object, [projectRoot]);
+  it('should call the runCLI method with the correct --projectRoot', async () => {
+    await sut.run({ jestConfig });
+    expect(runCLIStub).calledWith(sinon.match.object, [jestConfig.rootDir!]);
+  });
+
+  it('should call the runCLI method with --projectRoot = cwd when no rootDir is provided', async () => {
+    delete jestConfig.rootDir;
+    await sut.run({ jestConfig });
+    expect(runCLIStub).calledWith(sinon.match.object, [process.cwd()]);
   });
 
   it('should call the runCLI method with the --findRelatedTests flag when provided', async () => {
-    await sut.run({ jestConfig, projectRoot, fileNameUnderTest });
+    await sut.run({ jestConfig, fileNameUnderTest });
 
     expect(runCLIStub).calledWith(
       sinon.match({
         $0: 'stryker',
         _: [fileNameUnderTest],
-        config: JSON.stringify({ rootDir: projectRoot }),
+        config: JSON.stringify(jestConfig),
         findRelatedTests: true,
         runInBand: true,
         silent: true,
         testNamePattern: undefined,
       }),
-      [projectRoot]
+      [jestConfig.rootDir!]
     );
   });
 
   it('should call the runCLI method with the --testNamePattern flag when provided', async () => {
-    await sut.run({ jestConfig, projectRoot, testNamePattern: 'Foo should bar' });
+    await sut.run({ jestConfig, testNamePattern: 'Foo should bar' });
 
     expect(runCLIStub).calledWith(
       sinon.match({
         $0: 'stryker',
         _: [],
-        config: JSON.stringify({ rootDir: projectRoot }),
+        config: JSON.stringify(jestConfig),
         findRelatedTests: false,
         runInBand: true,
         silent: true,
         testNamePattern: 'Foo should bar',
       }),
-      [projectRoot]
+      [jestConfig.rootDir!]
     );
   });
 
   it('should call the runCLI method with the --testLocationInResults flag when provided', async () => {
-    await sut.run({ jestConfig, projectRoot, testLocationInResults: true });
+    await sut.run({ jestConfig, testLocationInResults: true });
 
     expect(runCLIStub).calledWith(
       sinon.match({
         testLocationInResults: true,
       }),
-      [projectRoot]
+      [jestConfig.rootDir!]
     );
   });
 
   it('should call the runCLI method without the --testLocationInResults flag when not', async () => {
-    await sut.run({ jestConfig, projectRoot, testLocationInResults: false });
-    expect(runCLIStub).calledWith(sinon.match({ testLocationInResults: false }), [projectRoot]);
+    await sut.run({ jestConfig, testLocationInResults: false });
+    expect(runCLIStub).calledWith(sinon.match({ testLocationInResults: false }), [jestConfig.rootDir!]);
   });
 
   it('should call the runCLI method and return the test result', async () => {
-    const result = await sut.run({ jestConfig, projectRoot });
+    const result = await sut.run({ jestConfig });
 
     expect(result).to.deep.equal({
       config: jestConfig,
@@ -90,7 +96,7 @@ describe(JestGreaterThan25TestAdapter.name, () => {
   });
 
   it('should call the runCLI method and return the test result when run with --findRelatedTests flag', async () => {
-    const result = await sut.run({ jestConfig, projectRoot, fileNameUnderTest });
+    const result = await sut.run({ jestConfig, fileNameUnderTest });
 
     expect(result).to.deep.equal({
       config: jestConfig,
diff --git a/packages/jest-runner/test/unit/jest-test-runner.spec.ts b/packages/jest-runner/test/unit/jest-test-runner.spec.ts
index 5754efc3ee..691cf6bc64 100644
--- a/packages/jest-runner/test/unit/jest-test-runner.spec.ts
+++ b/packages/jest-runner/test/unit/jest-test-runner.spec.ts
@@ -112,7 +112,7 @@ describe(JestTestRunner.name, () => {
       const sut = createSut();
       testInjector.logger.isTraceEnabled.returns(true);
       await sut.dryRun({ coverageAnalysis: 'off' });
-      expect(testInjector.logger.trace).calledWithMatch(/Invoking Jest with config\s.*/, sinon.match(/.*"jestConfig".*"projectRoot".*/));
+      expect(testInjector.logger.trace).calledWithMatch(/Invoking Jest with config\s.*/, sinon.match(/.*"jestConfig".*/));
     });
 
     it('should call the jestTestRunner run method and return a correct runResult', async () => {
@@ -481,7 +481,6 @@ describe(JestTestRunner.name, () => {
       expect(jestTestAdapterMock.run).calledWithExactly(
         sinon.match({
           jestConfig: sinon.match.object,
-          projectRoot: sinon.match.string,
           testNamePattern: undefined,
           fileNameUnderTest: '.stryker-tmp/sandbox2/foo.js',
         })
@@ -495,7 +494,6 @@ describe(JestTestRunner.name, () => {
       expect(jestTestAdapterMock.run).calledWithExactly(
         sinon.match({
           jestConfig: sinon.match.object,
-          projectRoot: sinon.match.string,
           testNamePattern: undefined,
           fileNameUnderTest: undefined,
         })
diff --git a/packages/jest-runner/test/unit/utils/create-react-jest-config.spec.ts b/packages/jest-runner/test/unit/utils/create-react-jest-config.spec.ts
deleted file mode 100644
index 201f24a6b6..0000000000
--- a/packages/jest-runner/test/unit/utils/create-react-jest-config.spec.ts
+++ /dev/null
@@ -1,40 +0,0 @@
-import { assert, expect } from 'chai';
-import sinon from 'sinon';
-
-import { createReactJestConfig, createReactTsJestConfig } from '../../../src/utils/create-react-jest-config';
-
-describe('create-jest-config', () => {
-  let requireStub: sinon.SinonStub;
-
-  beforeEach(() => {
-    requireStub = sinon.stub();
-    requireStub.returns(() => 'jestConfig');
-  });
-
-  describe('createReactJestConfig', () => {
-    it('should call the loader with the react jest config generator', () => {
-      // eslint-disable-next-line @typescript-eslint/no-empty-function
-      createReactJestConfig(() => {}, '/path/to/project', false, requireStub as unknown as NodeRequire);
-
-      assert(requireStub.calledWith('react-scripts/scripts/utils/createJestConfig'));
-    });
-
-    it('should return a jest config', () => {
-      // eslint-disable-next-line @typescript-eslint/no-empty-function
-      expect(createReactJestConfig(() => {}, '/path/to/project', false, requireStub as unknown as NodeRequire)).to.equal('jestConfig');
-    });
-  });
-  describe('createReactTsJestConfig', () => {
-    it('should call the loader with the react jest config generator', () => {
-      // eslint-disable-next-line @typescript-eslint/no-empty-function
-      createReactTsJestConfig(() => {}, '/path/to/project', false, requireStub as unknown as NodeRequire);
-
-      assert(requireStub.calledWith('react-scripts-ts/scripts/utils/createJestConfig'));
-    });
-
-    it('should return a jest config', () => {
-      // eslint-disable-next-line @typescript-eslint/no-empty-function
-      expect(createReactTsJestConfig(() => {}, '/path/to/project', false, requireStub as unknown as NodeRequire)).to.equal('jestConfig');
-    });
-  });
-});
diff --git a/packages/jest-runner/testResources/config-in-child-dir/client/jest.config.js b/packages/jest-runner/testResources/config-in-child-dir/client/jest.config.js
new file mode 100644
index 0000000000..3e253bb91c
--- /dev/null
+++ b/packages/jest-runner/testResources/config-in-child-dir/client/jest.config.js
@@ -0,0 +1,7 @@
+const project = "client"
+const prefix = "<rootDir>/../"
+
+module.exports = {
+  testEnvironment: "node",
+  testMatch: [prefix + project + "/**/*.test.js"],
+}
diff --git a/packages/jest-runner/testResources/config-in-child-dir/client/src/sum.js b/packages/jest-runner/testResources/config-in-child-dir/client/src/sum.js
new file mode 100644
index 0000000000..715ee7862c
--- /dev/null
+++ b/packages/jest-runner/testResources/config-in-child-dir/client/src/sum.js
@@ -0,0 +1,8 @@
+function sum(a, b) {
+  return a + b;
+}
+function sub(a, b) {
+  return a - b;
+}
+exports.sum = sum;
+exports.sub = sub;
diff --git a/packages/jest-runner/testResources/config-in-child-dir/client/src/sum.test.js b/packages/jest-runner/testResources/config-in-child-dir/client/src/sum.test.js
new file mode 100644
index 0000000000..56a145b981
--- /dev/null
+++ b/packages/jest-runner/testResources/config-in-child-dir/client/src/sum.test.js
@@ -0,0 +1,8 @@
+const {sum, sub} = require('./sum');
+
+test('adds 1 + 2 to equal 3', () => {
+  expect(sum(1, 2)).toBe(3);
+});
+test('sub 1 - 0 to equal 1', () => {
+  expect(sub(1, 0)).toBe(1);
+});