diff --git a/packages/runtime/src/__tests__/shell-exec.test.ts b/packages/runtime/src/__tests__/shell-exec.test.ts
index 18c1867772..49f7170210 100644
--- a/packages/runtime/src/__tests__/shell-exec.test.ts
+++ b/packages/runtime/src/__tests__/shell-exec.test.ts
@@ -23,7 +23,12 @@ import { existsSync, promises as fs } from 'node:fs';
 import { tmpdir } from 'node:os';
 import { join } from 'node:path';
 import { killWindowsTree } from '../process-tree-terminator.js';
-import { runProcessWithBoundedTail, runShellWithBoundedTail } from '../shell-exec.js';
+import {
+  buildUserCommandEnv,
+  runProcessWithBoundedTail,
+  runShellWithBoundedTail,
+} from '../shell-exec.js';
+import { defaultShellPlan } from '../shell-detect.js';
 
 const base = (over: Record<string, unknown> = {}) => ({
   cwd: process.cwd(),
@@ -71,6 +76,82 @@ function findPwsh(): string | undefined {
 }
 
 describe('runShellWithBoundedTail', () => {
+  test('removes Windows case variants without mutating the supplied environment', () => {
+    const input = {
+      ELECTRON_RUN_AS_NODE: 'upper',
+      electron_run_as_node: 'lower',
+      MAKA_SHELL_ENV_KEEP: 'kept',
+    };
+    const output = buildUserCommandEnv(input);
+    if (process.platform === 'win32') {
+      assert.deepEqual(output, { MAKA_SHELL_ENV_KEEP: 'kept' });
+    } else {
+      assert.deepEqual(output, {
+        electron_run_as_node: 'lower',
+        MAKA_SHELL_ENV_KEEP: 'kept',
+      });
+    }
+    assert.deepEqual(input, {
+      ELECTRON_RUN_AS_NODE: 'upper',
+      electron_run_as_node: 'lower',
+      MAKA_SHELL_ENV_KEEP: 'kept',
+    });
+  });
+
+  test('clears inherited Electron Node mode at the user-command boundary', async () => {
+    const previousElectronRunAsNode = process.env.ELECTRON_RUN_AS_NODE;
+    const previousKeep = process.env.MAKA_SHELL_ENV_KEEP;
+    process.env.ELECTRON_RUN_AS_NODE = '1';
+    process.env.MAKA_SHELL_ENV_KEEP = 'kept-by-parent';
+    try {
+      const childEnv = buildUserCommandEnv(process.env);
+      assert.equal(childEnv.ELECTRON_RUN_AS_NODE, undefined);
+      assert.equal(childEnv.MAKA_SHELL_ENV_KEEP, 'kept-by-parent');
+
+      const result = await runShellWithBoundedTail(
+        shellEnvironmentProbeCommand(),
+        base({ env: process.env, shell: defaultShellPlan() }),
+      );
+      assert.equal(result.exitCode, 0);
+      assert.match(result.stdout, /electron=\r?\n/u);
+      assert.match(result.stdout, /keep=kept-by-parent/u);
+      assert.match(result.stdout, /explicit=explicit/u);
+      assert.equal(process.env.ELECTRON_RUN_AS_NODE, '1');
+      assert.equal(process.env.MAKA_SHELL_ENV_KEEP, 'kept-by-parent');
+    } finally {
+      if (previousElectronRunAsNode === undefined) delete process.env.ELECTRON_RUN_AS_NODE;
+      else process.env.ELECTRON_RUN_AS_NODE = previousElectronRunAsNode;
+      if (previousKeep === undefined) delete process.env.MAKA_SHELL_ENV_KEEP;
+      else process.env.MAKA_SHELL_ENV_KEEP = previousKeep;
+    }
+  });
+
+  test('clears inherited Electron Node mode for direct argv commands', async () => {
+    const previousElectronRunAsNode = process.env.ELECTRON_RUN_AS_NODE;
+    const previousKeep = process.env.MAKA_SHELL_ENV_KEEP;
+    process.env.ELECTRON_RUN_AS_NODE = '1';
+    process.env.MAKA_SHELL_ENV_KEEP = 'kept-by-parent';
+    try {
+      const result = await runProcessWithBoundedTail(
+        process.execPath,
+        [
+          '-e',
+          "process.stdout.write(`electron=${process.env.ELECTRON_RUN_AS_NODE ?? ''}\\nkeep=${process.env.MAKA_SHELL_ENV_KEEP ?? ''}`)",
+        ],
+        base({ env: process.env }),
+      );
+      assert.equal(result.exitCode, 0);
+      assert.equal(result.stdout, 'electron=\nkeep=kept-by-parent');
+      assert.equal(process.env.ELECTRON_RUN_AS_NODE, '1');
+      assert.equal(process.env.MAKA_SHELL_ENV_KEEP, 'kept-by-parent');
+    } finally {
+      if (previousElectronRunAsNode === undefined) delete process.env.ELECTRON_RUN_AS_NODE;
+      else process.env.ELECTRON_RUN_AS_NODE = previousElectronRunAsNode;
+      if (previousKeep === undefined) delete process.env.MAKA_SHELL_ENV_KEEP;
+      else process.env.MAKA_SHELL_ENV_KEEP = previousKeep;
+    }
+  });
+
   test('writes a legacy WSL Bash command through stdin', {
     skip: process.platform === 'win32' ? 'uses /bin/sh as a portable stdin probe' : false,
   }, async () => {
@@ -349,3 +430,14 @@ describe('runShellWithBoundedTail', () => {
     assert.equal(await killWindowsTree(999_999), false);
   });
 });
+
+function shellEnvironmentProbeCommand(): string {
+  const shell = defaultShellPlan();
+  if (shell.kind === 'cmd') {
+    return 'echo electron=%ELECTRON_RUN_AS_NODE% & echo keep=%MAKA_SHELL_ENV_KEEP% & set ELECTRON_RUN_AS_NODE=explicit & call echo explicit=%%ELECTRON_RUN_AS_NODE%%';
+  }
+  if (shell.kind === 'pwsh' || shell.kind === 'powershell') {
+    return 'Write-Output "electron=$env:ELECTRON_RUN_AS_NODE"; Write-Output "keep=$env:MAKA_SHELL_ENV_KEEP"; $env:ELECTRON_RUN_AS_NODE=\'explicit\'; Write-Output "explicit=$env:ELECTRON_RUN_AS_NODE"';
+  }
+  return 'printf \'electron=%s\\nkeep=%s\\n\' "${ELECTRON_RUN_AS_NODE-}" "$MAKA_SHELL_ENV_KEEP"; ELECTRON_RUN_AS_NODE=explicit; printf \'explicit=%s\\n\' "$ELECTRON_RUN_AS_NODE"';
+}
diff --git a/packages/runtime/src/__tests__/shell-run-manager.test.ts b/packages/runtime/src/__tests__/shell-run-manager.test.ts
index a462b1363e..8a072b4fb2 100644
--- a/packages/runtime/src/__tests__/shell-run-manager.test.ts
+++ b/packages/runtime/src/__tests__/shell-run-manager.test.ts
@@ -173,6 +173,70 @@ describe('ShellRunProcessManager', () => {
     assert.equal(manager.liveCount(), 0);
   });
 
+  test('clears inherited Electron Node mode for background pipes, PTY, and argv', async () => {
+    const previousElectronRunAsNode = process.env.ELECTRON_RUN_AS_NODE;
+    const previousKeep = process.env.MAKA_SHELL_ENV_KEEP;
+    process.env.ELECTRON_RUN_AS_NODE = '1';
+    process.env.MAKA_SHELL_ENV_KEEP = 'kept-by-parent';
+    let manager: ShellRunProcessManager | undefined;
+    try {
+      manager = await createTestManager();
+      const cwd = await workspace();
+      const probeScript =
+        "process.stdout.write(`electron=${process.env.ELECTRON_RUN_AS_NODE ?? '<missing>'}\\nkeep=${process.env.MAKA_SHELL_ENV_KEEP ?? '<missing>'}\\n`)";
+      const command = nodeCommand(probeScript);
+
+      const pipe = await manager.runBackgroundBash(shellInput({ cwd, command, timeoutMs: 10_000 }));
+      assert.equal(pipe.kind, 'shell_run');
+      const pipeResult = await waitForTerminalShellRun(manager, pipe.ref);
+      assert.equal(pipeResult.status, 'completed');
+      assert.equal(pipeResult.output?.mode, 'pipes');
+      if (pipeResult.output?.mode !== 'pipes') throw new Error('expected pipe output');
+      assert.match(pipeResult.output.stdout, /electron=<missing>/u);
+      assert.match(pipeResult.output.stdout, /keep=kept-by-parent/u);
+
+      const argv = await manager.runBackgroundBash(
+        shellInput({
+          cwd,
+          command: 'direct argv probe',
+          argv: [process.execPath, '-e', probeScript],
+          timeoutMs: 10_000,
+        }),
+      );
+      assert.equal(argv.kind, 'shell_run');
+      const argvResult = await waitForTerminalShellRun(manager, argv.ref);
+      assert.equal(argvResult.status, 'completed');
+      assert.equal(argvResult.output?.mode, 'pipes');
+      if (argvResult.output?.mode !== 'pipes') throw new Error('expected pipe output');
+      assert.match(argvResult.output.stdout, /electron=<missing>/u);
+      assert.match(argvResult.output.stdout, /keep=kept-by-parent/u);
+
+      const pty = await manager.runBackgroundBash(
+        shellInput({ cwd, command, pty: true, timeoutMs: 10_000 }),
+      );
+      assert.equal(pty.kind, 'shell_run');
+      const ptyResult = await waitForTerminalShellRun(manager, pty.ref);
+      assert.equal(ptyResult.status, 'completed');
+      assert.equal(ptyResult.output?.mode, 'pty');
+      if (ptyResult.output?.mode !== 'pty') throw new Error('expected PTY output');
+      const ptyText = terminalText(ptyResult.output);
+      assert.match(ptyText, /electron=<missing>/u);
+      assert.match(ptyText, /keep=kept-by-parent/u);
+
+      assert.equal(process.env.ELECTRON_RUN_AS_NODE, '1');
+      assert.equal(process.env.MAKA_SHELL_ENV_KEEP, 'kept-by-parent');
+    } finally {
+      try {
+        await manager?.terminateAll();
+      } finally {
+        if (previousElectronRunAsNode === undefined) delete process.env.ELECTRON_RUN_AS_NODE;
+        else process.env.ELECTRON_RUN_AS_NODE = previousElectronRunAsNode;
+        if (previousKeep === undefined) delete process.env.MAKA_SHELL_ENV_KEEP;
+        else process.env.MAKA_SHELL_ENV_KEEP = previousKeep;
+      }
+    }
+  });
+
   test('preserves CJK PowerShell output through pipes', {
     skip: process.platform === 'win32' ? false : 'Windows PowerShell 5.1 regression',
   }, async () => {
diff --git a/packages/runtime/src/shell-exec.ts b/packages/runtime/src/shell-exec.ts
index d277aee75d..809106f9ce 100644
--- a/packages/runtime/src/shell-exec.ts
+++ b/packages/runtime/src/shell-exec.ts
@@ -57,6 +57,8 @@ export const BASH_MAX_RETAINED_CHARS = 1024 * 1024;
 // chunks keep flowing into the retained tail buffer.
 export const BASH_MAX_LIVE_EMIT_CHARS = 1024 * 1024;
 
+const ELECTRON_RUN_AS_NODE = 'ELECTRON_RUN_AS_NODE';
+
 // Emitted once per stream when live forwarding is suppressed. The full output is
 // not lost — it still feeds the retained tail and the returned result.
 export const LIVE_OUTPUT_SUPPRESSED_MARKER =
@@ -119,6 +121,23 @@ export interface BoundedShellResult {
   aborted: boolean;
 }
 
+/**
+ * Build the environment boundary for a user command without changing the
+ * Runtime Host's own environment. Electron uses this variable to put the
+ * current process in Node mode; inheriting it would make Electron-launched
+ * user programs lose Electron APIs such as BrowserWindow. Windows environment
+ * names are case-insensitive, while POSIX environment names are not.
+ */
+export function buildUserCommandEnv(env: NodeJS.ProcessEnv = process.env): NodeJS.ProcessEnv {
+  return Object.fromEntries(
+    Object.entries(env).filter(([key]) =>
+      process.platform === 'win32'
+        ? key.toUpperCase() !== ELECTRON_RUN_AS_NODE
+        : key !== ELECTRON_RUN_AS_NODE,
+    ),
+  );
+}
+
 /**
  * Run `command` in a shell, streaming output into a memory-bounded tail. Never
  * kills the command for producing too much output — it keeps only the last
@@ -131,18 +150,15 @@ export function runShellWithBoundedTail(
   command: string,
   options: BoundedShellOptions,
 ): Promise<BoundedShellResult> {
-  const plan = buildShellSpawnPlan(
-    options.shell ?? defaultShellPlan(),
-    command,
-    options.env ?? process.env,
-  );
+  const env = buildUserCommandEnv(options.env ?? process.env);
+  const plan = buildShellSpawnPlan(options.shell ?? defaultShellPlan(), command, env);
   return runSpawnedProcessWithBoundedTail(
     plan.file,
     plan.args,
     plan.useShellOption,
     {
       ...options,
-      ...(plan.env ? { env: plan.env } : {}),
+      env: plan.env ?? env,
     },
     plan.stdin,
   );
@@ -154,7 +170,10 @@ export function runProcessWithBoundedTail(
   args: readonly string[],
   options: BoundedShellOptions,
 ): Promise<BoundedShellResult> {
-  return runSpawnedProcessWithBoundedTail(program, args, false, options);
+  return runSpawnedProcessWithBoundedTail(program, args, false, {
+    ...options,
+    env: buildUserCommandEnv(options.env ?? process.env),
+  });
 }
 
 function runSpawnedProcessWithBoundedTail(
diff --git a/packages/runtime/src/shell-run-manager.ts b/packages/runtime/src/shell-run-manager.ts
index 6ab56d666e..13fecafe5c 100644
--- a/packages/runtime/src/shell-run-manager.ts
+++ b/packages/runtime/src/shell-run-manager.ts
@@ -39,6 +39,7 @@ import {
   BASH_MAX_LIVE_EMIT_CHARS,
   BASH_MAX_RETAINED_CHARS,
   LIVE_OUTPUT_SUPPRESSED_MARKER,
+  buildUserCommandEnv,
 } from './shell-exec.js';
 import {
   DEFAULT_PROCESS_TERMINATION_GRACE_MS,
@@ -735,6 +736,7 @@ export class ShellRunProcessManager
     sessionEpoch: number,
     onLiveAdmission: ((live: LiveShellRun) => void) | undefined,
   ): Promise<LivePipeShellRun> {
+    const env = buildUserCommandEnv(input.env ?? process.env);
     const collector = new PipeTailCollector(this.maxRetainedChars);
     const pending: Array<(live: LivePipeShellRun) => void> = [];
     let live: LivePipeShellRun | undefined;
@@ -751,11 +753,7 @@ export class ShellRunProcessManager
             args: [...input.argv.slice(1)],
             useShellOption: false,
           }
-        : buildShellSpawnPlan(
-            input.shell ?? defaultShellPlan(),
-            input.command,
-            input.env ?? process.env,
-          );
+        : buildShellSpawnPlan(input.shell ?? defaultShellPlan(), input.command, env);
       startingRecord = await this.createStartingRecord(
         input,
         shellRunId,
@@ -767,7 +765,7 @@ export class ShellRunProcessManager
       const driver = new PipeProcessDriver({
         plan,
         cwd: input.cwd,
-        ...((plan.env ?? input.env) ? { env: plan.env ?? input.env } : {}),
+        env: plan.env ?? env,
         ...(input.fdInputs ? { fdInputs: input.fdInputs } : {}),
         outputDrainMs: this.pipeOutputDrainMs,
         onData: (stream, data) => dispatch((target) => this.onPipeData(target, stream, data)),
@@ -813,6 +811,7 @@ export class ShellRunProcessManager
     slotReservation: ShellRunSlotReservation,
     sessionEpoch: number,
   ): Promise<LivePtyShellRun> {
+    const env = buildUserCommandEnv(input.env ?? process.env);
     const pending: Array<(live: LivePtyShellRun) => void> = [];
     let live: LivePtyShellRun | undefined;
     let driver: PtyProcessDriver | undefined;
@@ -836,11 +835,7 @@ export class ShellRunProcessManager
         onDirty: () => dispatch((target) => this.scheduleAutomaticFlush(target)),
         onFailure: (error) => dispatch((target) => this.handleIntegrityFailure(target, error)),
       });
-      const plan = buildPtyShellSpawnPlan(
-        input.shell ?? defaultShellPlan(),
-        input.command,
-        input.env ?? process.env,
-      );
+      const plan = buildPtyShellSpawnPlan(input.shell ?? defaultShellPlan(), input.command, env);
       startingRecord = await this.createStartingRecord(
         input,
         shellRunId,
@@ -853,7 +848,7 @@ export class ShellRunProcessManager
         file: plan.file,
         args: plan.args,
         cwd: input.cwd,
-        env: plan.env ?? input.env ?? process.env,
+        env: plan.env ?? env,
         cols: PTY_INITIAL_COLS,
         rows: PTY_INITIAL_ROWS,
         onData: (data) => dispatch((target) => this.onPtyData(target, data)),