diff --git a/apps/cli/lib/daemon-client.ts b/apps/cli/lib/daemon-client.ts
index 5b7b1e5416..5004c35680 100644
--- a/apps/cli/lib/daemon-client.ts
+++ b/apps/cli/lib/daemon-client.ts
@@ -11,6 +11,7 @@ import {
 	PROCESS_MANAGER_EVENTS_SOCKET_PATH,
 	PROCESS_MANAGER_CONTROL_SOCKET_PATH,
 	PROCESS_MANAGER_HOME,
+	daemonPipePath,
 } from 'cli/lib/paths';
 import { SocketStreamClient, SocketMessageDecoder, SocketRequestClient } from 'cli/lib/socket';
 import {
@@ -33,7 +34,7 @@ const CONNECTION_TIMEOUT_MS = 10_000;
 const PROCESS_MANAGER_LOCKFILE_PATH = path.join( PROCESS_MANAGER_HOME, 'pm-connection.lock' );
 export const SITE_EVENTS_SOCKET_PATH =
 	process.platform === 'win32'
-		? '\\\\.\\pipe\\studio-events.sock'
+		? daemonPipePath( 'studio-events' )
 		: path.join( PROCESS_MANAGER_HOME, 'events.sock' );
 
 function ensureProcessManagerHome() {
diff --git a/apps/cli/lib/native-php/config.ts b/apps/cli/lib/native-php/config.ts
index bb6fa39a0d..23d4445c4d 100644
--- a/apps/cli/lib/native-php/config.ts
+++ b/apps/cli/lib/native-php/config.ts
@@ -6,6 +6,7 @@ import { NativePhpSupportedVersion } from '@studio/common/lib/php-binary-metadat
 import { writeFile } from 'atomically';
 import semver from 'semver';
 import { getPhpBinaryPath } from '../dependency-management/paths';
+import { getPhpSafeTmpDir } from './tmp-dir';
 
 // Disabled to shrink the attack surface available to PHP code running inside a
 // Studio site. Each entry falls into one of:
@@ -215,13 +216,9 @@ function getOpcacheRootDir(): string {
 		return opcacheRootDir;
 	}
 
-	// Resolve to the long-form path on Windows. `os.tmpdir()` can return an 8.3
-	// short name (e.g. C:\Users\BUILDK~1\AppData\…) when the user has a long
-	// username, and PHP's INI scanner treats `~` as a special token, breaking
-	// `-d opcache.file_cache=<path>` parsing.
-	const tmpRoot =
-		process.platform === 'win32' ? fs.realpathSync.native( os.tmpdir() ) : os.tmpdir();
-	opcacheRootDir = fs.mkdtempSync( path.join( tmpRoot, 'studio-opcache-' ) );
+	// `getPhpSafeTmpDir()` resolves the Windows 8.3 short name so PHP's INI scanner
+	// doesn't choke on the `~` in `-d opcache.file_cache=<path>`.
+	opcacheRootDir = fs.mkdtempSync( path.join( getPhpSafeTmpDir(), 'studio-opcache-' ) );
 	const dirToClean = opcacheRootDir;
 	process.once( 'exit', () => {
 		try {
@@ -292,7 +289,9 @@ export function getDefaultPhpArgs(
 	// runtime.php (constants, SQLite loader, upload proxy) into imported sites
 	// without modifying their wp-config.php.
 	if ( autoPrependFile ) {
-		args.push( '-d', `auto_prepend_file=${ autoPrependFile }` );
+		// Quote the path so a space (or other INI-special char) in it can't break parsing,
+		// matching the other `-d` directives above.
+		args.push( '-d', `auto_prepend_file="${ autoPrependFile }"` );
 	}
 
 	return args;
diff --git a/apps/cli/lib/native-php/phpmyadmin.ts b/apps/cli/lib/native-php/phpmyadmin.ts
index 15136a160a..9368945a90 100644
--- a/apps/cli/lib/native-php/phpmyadmin.ts
+++ b/apps/cli/lib/native-php/phpmyadmin.ts
@@ -1,6 +1,6 @@
 import fs from 'node:fs';
-import os from 'node:os';
 import path from 'node:path';
+import { getPhpSafeTmpDir } from './tmp-dir';
 import type { ServerConfig } from 'cli/lib/types/wordpress-server-ipc';
 
 function phpStringLiteral( value: string ): string {
@@ -9,12 +9,13 @@ function phpStringLiteral( value: string ): string {
 
 export function getNativePhpMyAdminWpEnvPath( config: Pick< ServerConfig, 'siteId' > ): string {
 	const safeSiteId = config.siteId.replace( /[^a-zA-Z0-9._-]/g, '-' );
-	return path.join( os.tmpdir(), 'studio-phpmyadmin-wp-env', safeSiteId, 'wp-env.php' );
+	// getPhpSafeTmpDir() avoids the Windows 8.3 `~` short name; this path reaches PHP.
+	return path.join( getPhpSafeTmpDir(), 'studio-phpmyadmin-wp-env', safeSiteId, 'wp-env.php' );
 }
 
 export function getPhpMyAdminSessionPath( config: Pick< ServerConfig, 'siteId' > ): string {
 	const safeSiteId = config.siteId.replace( /[^a-zA-Z0-9._-]/g, '-' );
-	return path.join( os.tmpdir(), 'studio-phpmyadmin-sessions', safeSiteId );
+	return path.join( getPhpSafeTmpDir(), 'studio-phpmyadmin-sessions', safeSiteId );
 }
 
 export async function writeNativePhpMyAdminWpEnv( config: ServerConfig ): Promise< string > {
diff --git a/apps/cli/lib/native-php/site-setup.ts b/apps/cli/lib/native-php/site-setup.ts
index 9337c193f0..68eb89da93 100644
--- a/apps/cli/lib/native-php/site-setup.ts
+++ b/apps/cli/lib/native-php/site-setup.ts
@@ -1,11 +1,11 @@
 import fs from 'node:fs';
-import os from 'node:os';
 import path from 'node:path';
 import { DEFAULT_LOCALE } from '@studio/common/lib/locale';
 import { escapePhpSingleQuotedString } from '@studio/common/lib/mu-plugins';
 import { decodePassword } from '@studio/common/lib/passwords';
 import { getWpCliPharPath } from 'cli/lib/dependency-management/paths';
 import { runPhpCommand } from './php-process';
+import { getPhpSafeTmpDir } from './tmp-dir';
 import type { NativePhpSupportedVersion } from '@studio/common/lib/php-binary-metadata';
 import type { ServerConfig } from 'cli/lib/types/wordpress-server-ipc';
 
@@ -99,7 +99,9 @@ export function writeSiteUrlPrependFile(
 	siteUrl: string,
 	originalAutoPrependFile?: string
 ): string {
-	const dir = fs.mkdtempSync( path.join( os.tmpdir(), 'studio-siteurl-prepend-' ) );
+	// getPhpSafeTmpDir() avoids the Windows 8.3 `~` short name; this path is handed to PHP as
+	// auto_prepend_file, and a `~` in it breaks the parser with `syntax error, unexpected '~'`.
+	const dir = fs.mkdtempSync( path.join( getPhpSafeTmpDir(), 'studio-siteurl-prepend-' ) );
 	const prependPath = path.join( dir, 'prepend.php' );
 	fs.writeFileSync( prependPath, getSiteUrlPrependContent( siteUrl, originalAutoPrependFile ) );
 	return prependPath;
diff --git a/apps/cli/lib/native-php/tmp-dir.ts b/apps/cli/lib/native-php/tmp-dir.ts
new file mode 100644
index 0000000000..9aff6cb3fc
--- /dev/null
+++ b/apps/cli/lib/native-php/tmp-dir.ts
@@ -0,0 +1,14 @@
+import fs from 'node:fs';
+import os from 'node:os';
+
+// Returns `os.tmpdir()` resolved to its long-form path on Windows.
+//
+// When the OS account name is longer than 8 characters (e.g. CI's `buildkite-agent`),
+// Windows exposes an 8.3 short name and `os.tmpdir()` can return something like
+// `C:\Users\BUILDK~1\AppData\Local\Temp`. PHP's INI/argument scanner treats the `~` as a
+// special token, so any temp path we hand to PHP — auto_prepend_file, opcache.file_cache,
+// the phpMyAdmin config, … — breaks with `syntax error, unexpected '~'`. Resolving to the
+// long form removes the tilde. No-op on macOS/Linux, which don't have 8.3 short names.
+export function getPhpSafeTmpDir(): string {
+	return process.platform === 'win32' ? fs.realpathSync.native( os.tmpdir() ) : os.tmpdir();
+}
diff --git a/apps/cli/lib/paths.ts b/apps/cli/lib/paths.ts
index 14f068599d..7810f04268 100644
--- a/apps/cli/lib/paths.ts
+++ b/apps/cli/lib/paths.ts
@@ -1,16 +1,35 @@
+import crypto from 'crypto';
 import os from 'os';
 import path from 'path';
 
 export const STUDIO_CLI_HOME = path.join( os.homedir(), '.studio' );
 
+export const DEFAULT_PROCESS_MANAGER_HOME = path.join( STUDIO_CLI_HOME, 'daemon' );
+
 export const PROCESS_MANAGER_HOME =
-	process.env.STUDIO_PROCESS_MANAGER_HOME ?? path.join( STUDIO_CLI_HOME, 'daemon' );
+	process.env.STUDIO_PROCESS_MANAGER_HOME ?? DEFAULT_PROCESS_MANAGER_HOME;
 export const PROCESS_MANAGER_LOGS_DIR = path.join( PROCESS_MANAGER_HOME, 'logs' );
+
+// Windows named pipes live in a single, flat, machine-global namespace — unlike Unix domain sockets,
+// they can't be nested under PROCESS_MANAGER_HOME. A fixed pipe name therefore makes every process on
+// the machine bind/connect to the SAME daemon regardless of PROCESS_MANAGER_HOME, silently defeating
+// the per-run isolation that setting STUDIO_PROCESS_MANAGER_HOME gives on macOS/Linux (and that the CLI
+// test harness relies on). Derive the pipe name from the home when a custom one is set, so isolation
+// works on Windows too. The default home keeps its original fixed name, so the shipping desktop app and
+// CLI still share a single daemon exactly as before.
+export function daemonPipePath( baseName: string, home: string = PROCESS_MANAGER_HOME ): string {
+	if ( home === DEFAULT_PROCESS_MANAGER_HOME ) {
+		return `\\\\.\\pipe\\${ baseName }.sock`;
+	}
+	const homeHash = crypto.createHash( 'sha1' ).update( home ).digest( 'hex' ).slice( 0, 12 );
+	return `\\\\.\\pipe\\${ baseName }-${ homeHash }.sock`;
+}
+
 export const PROCESS_MANAGER_CONTROL_SOCKET_PATH =
 	process.platform === 'win32'
-		? '\\\\.\\pipe\\studio-daemon.sock'
+		? daemonPipePath( 'studio-daemon' )
 		: path.join( PROCESS_MANAGER_HOME, 'daemon.sock' );
 export const PROCESS_MANAGER_EVENTS_SOCKET_PATH =
 	process.platform === 'win32'
-		? '\\\\.\\pipe\\studio-daemon-events.sock'
+		? daemonPipePath( 'studio-daemon-events' )
 		: path.join( PROCESS_MANAGER_HOME, 'daemon-events.sock' );
diff --git a/apps/cli/tests/paths.test.ts b/apps/cli/tests/paths.test.ts
new file mode 100644
index 0000000000..fb1aa88ba6
--- /dev/null
+++ b/apps/cli/tests/paths.test.ts
@@ -0,0 +1,39 @@
+import { describe, expect, it } from 'vitest';
+import { DEFAULT_PROCESS_MANAGER_HOME, daemonPipePath } from '../lib/paths';
+
+describe( 'daemonPipePath (Windows daemon socket isolation)', () => {
+	it( 'keeps the original fixed pipe name for the default home (desktop/CLI still share one daemon)', () => {
+		expect( daemonPipePath( 'studio-daemon', DEFAULT_PROCESS_MANAGER_HOME ) ).toBe(
+			'\\\\.\\pipe\\studio-daemon.sock'
+		);
+		expect( daemonPipePath( 'studio-daemon-events', DEFAULT_PROCESS_MANAGER_HOME ) ).toBe(
+			'\\\\.\\pipe\\studio-daemon-events.sock'
+		);
+	} );
+
+	it( 'derives a per-home pipe name for a custom home so runs are isolated on Windows', () => {
+		const a = daemonPipePath( 'studio-daemon', 'C:\\Temp\\home-a' );
+		const b = daemonPipePath( 'studio-daemon', 'C:\\Temp\\home-b' );
+
+		expect( a ).toMatch( /^\\\\\.\\pipe\\studio-daemon-[0-9a-f]{12}\.sock$/ );
+		expect( a ).not.toBe( b );
+		// Two custom homes must not collide with the default fixed pipe either.
+		expect( a ).not.toBe( '\\\\.\\pipe\\studio-daemon.sock' );
+	} );
+
+	it( 'is deterministic for a given home so repeated CLI invocations reach the same daemon', () => {
+		expect( daemonPipePath( 'studio-daemon', 'C:\\Temp\\home-a' ) ).toBe(
+			daemonPipePath( 'studio-daemon', 'C:\\Temp\\home-a' )
+		);
+	} );
+
+	it( 'namespaces distinct sockets so control/events/site-events do not collide for the same home', () => {
+		const home = 'C:\\Temp\\home-a';
+		const names = new Set( [
+			daemonPipePath( 'studio-daemon', home ),
+			daemonPipePath( 'studio-daemon-events', home ),
+			daemonPipePath( 'studio-events', home ),
+		] );
+		expect( names.size ).toBe( 3 );
+	} );
+} );