diff --git a/scripts/stryker-diff.mjs b/scripts/stryker-diff.mjs
index c0e8a6cd1a..32211ebbd6 100644
--- a/scripts/stryker-diff.mjs
+++ b/scripts/stryker-diff.mjs
@@ -313,6 +313,10 @@ export function resolveVitestBinary(repoRoot, packageEntry) {
 	return candidates.find((candidate) => fs.existsSync(candidate)) ?? candidates.at(-1)
 }
 
+export function resolveStrykerTempDir(repoRoot, runRoot) {
+	return path.relative(runRoot, path.join(repoRoot, ".stryker-tmp")) || ".stryker-tmp"
+}
+
 export function discoverRelatedTestFiles(repoRoot, packageEntry, reportDirectory) {
 	const packageRoot = path.join(repoRoot, packageEntry.root)
 	const runRoot = path.join(repoRoot, packageEntry.runRoot ?? packageEntry.root)
@@ -378,6 +382,7 @@ function runStryker(repoRoot, packageEntry, reportRoot, dryRunOnly) {
 				.relative(runRoot, path.join(packageRoot, packageEntry.vitestConfig))
 				.replaceAll("\\", "/"),
 			STRYKER_REPORT_DIR: reportDirectory,
+			STRYKER_TEMP_DIR: resolveStrykerTempDir(repoRoot, runRoot),
 			STRYKER_IN_PLACE: "false",
 			STRYKER_VITEST_RELATED: packageEntry.vitestRelated === false ? "false" : "true",
 			STRYKER_TEST_FILES: JSON.stringify(packageEntry.testFiles ?? []),
diff --git a/scripts/stryker-diff.test.mjs b/scripts/stryker-diff.test.mjs
index 0f39dc507f..80b04e2a51 100644
--- a/scripts/stryker-diff.test.mjs
+++ b/scripts/stryker-diff.test.mjs
@@ -4,7 +4,7 @@ import fs from "node:fs"
 import os from "node:os"
 import path from "node:path"
 import { describe, it } from "node:test"
-import { fileURLToPath } from "node:url"
+import { fileURLToPath, pathToFileURL } from "node:url"
 
 import {
 	MAX_CHANGED_LINES,
@@ -23,6 +23,7 @@ import {
 	parseNameStatus,
 	parseVitestTestFiles,
 	preferDirectTestFiles,
+	resolveStrykerTempDir,
 	resolveVitestBinary,
 	packageForPath,
 	runManifest,
@@ -211,6 +212,11 @@ describe("preferDirectTestFiles", () => {
 })
 
 describe("related-test discovery", () => {
+	it("keeps Stryker's temp directory relative to each run root", () => {
+		assert.equal(resolveStrykerTempDir("/repo", "/repo"), ".stryker-tmp")
+		assert.equal(resolveStrykerTempDir("/repo", "/repo/src"), path.join("..", ".stryker-tmp"))
+	})
+
 	it("resolves Vitest from each package before falling back to the repository", () => {
 		const repo = fs.mkdtempSync(path.join(os.tmpdir(), "stryker-vitest-"))
 		const extension = PACKAGE_CONFIGS.find(({ id }) => id === "extension")
@@ -259,6 +265,26 @@ describe("related-test discovery", () => {
 	})
 })
 
+describe("Stryker configuration", () => {
+	it("uses the default or configured temp directory", async () => {
+		const originalTempDir = process.env.STRYKER_TEMP_DIR
+		const configUrl = pathToFileURL(path.join(repositoryRoot, "stryker.config.mjs"))
+
+		try {
+			delete process.env.STRYKER_TEMP_DIR
+			const defaultConfig = (await import(`${configUrl.href}?temp-dir=default`)).default
+			assert.equal(defaultConfig.tempDirName, ".stryker-tmp")
+
+			process.env.STRYKER_TEMP_DIR = path.join("..", ".stryker-tmp")
+			const configuredConfig = (await import(`${configUrl.href}?temp-dir=configured`)).default
+			assert.equal(configuredConfig.tempDirName, path.join("..", ".stryker-tmp"))
+		} finally {
+			if (originalTempDir === undefined) delete process.env.STRYKER_TEMP_DIR
+			else process.env.STRYKER_TEMP_DIR = originalTempDir
+		}
+	})
+})
+
 describe("selectFromGit", () => {
 	it("derives changed executable ranges from the base/head merge base", () => {
 		const repo = fs.mkdtempSync(path.join(os.tmpdir(), "stryker-diff-"))
diff --git a/src/eslint.config.mjs b/src/eslint.config.mjs
index bd41ff807b..7120f2e875 100644
--- a/src/eslint.config.mjs
+++ b/src/eslint.config.mjs
@@ -58,6 +58,6 @@ export default [
 		},
 	},
 	{
-		ignores: ["webview-ui", "out"],
+		ignores: [".stryker-tmp", "webview-ui", "out"],
 	},
 ]
diff --git a/src/tsconfig.json b/src/tsconfig.json
index 255fa2b8a4..c62520e8ae 100644
--- a/src/tsconfig.json
+++ b/src/tsconfig.json
@@ -21,12 +21,12 @@
 		"useUnknownInCatchVariables": false
 	},
 	"include": ["."],
-	"exclude": ["node_modules"],
+	"exclude": ["**/.stryker-tmp", "node_modules"],
 	"watchOptions": {
 		"watchFile": "useFsEvents",
 		"watchDirectory": "useFsEvents",
 		"fallbackPolling": "dynamicPriority",
 		"synchronousWatchDirectory": true,
-		"excludeDirectories": ["**/node_modules", "**/dist", "**/.turbo"]
+		"excludeDirectories": ["**/node_modules", "**/dist", "**/.stryker-tmp", "**/.turbo"]
 	}
 }
diff --git a/stryker.config.mjs b/stryker.config.mjs
index c1a652e7c1..7d85640377 100644
--- a/stryker.config.mjs
+++ b/stryker.config.mjs
@@ -1,5 +1,6 @@
 const vitestConfig = process.env.STRYKER_VITEST_CONFIG ?? "vitest.config.ts"
 const reportDirectory = process.env.STRYKER_REPORT_DIR ?? "reports/mutation"
+const tempDirName = process.env.STRYKER_TEMP_DIR ?? ".stryker-tmp"
 const testFiles = JSON.parse(process.env.STRYKER_TEST_FILES ?? "[]")
 
 export default {
@@ -12,6 +13,7 @@ export default {
 	testFiles,
 	incremental: false,
 	inPlace: process.env.STRYKER_IN_PLACE === "true",
+	tempDirName,
 	concurrency: 2,
 	timeoutMS: 5_000,
 	timeoutFactor: 1.5,