diff --git a/config/scripts/ensure-native-runtime.mjs b/config/scripts/ensure-native-runtime.mjs
index c45027521..6530ba755 100644
--- a/config/scripts/ensure-native-runtime.mjs
+++ b/config/scripts/ensure-native-runtime.mjs
@@ -49,7 +49,7 @@ function readRuntimeArg() {
 }
 
 function ensureNodeRuntime() {
-  const initial = runCurrentProcessCheck()
+  const initial = runNodeCheck()
   if (initial.ok) {
     return
   }
@@ -61,7 +61,7 @@ function ensureNodeRuntime() {
   printCheckError(initial)
   runPnpm(['rebuild', ...failedModules])
 
-  const final = runCurrentProcessCheck()
+  const final = runNodeCheck()
   if (!final.ok) {
     console.error(
       `[native-runtime] Native modules still do not load for ${formatRuntimeLabel('node')}.`
@@ -93,12 +93,16 @@ function ensureElectronRuntime() {
   }
 }
 
-function runCurrentProcessCheck() {
-  const failures = collectNativeModuleFailures()
-  if (failures.length === 0) {
-    return { ok: true, failures }
-  }
-  return { ok: false, failures }
+function runNodeCheck() {
+  // Why: a failed native addon load can poison the current process, so the
+  // post-rebuild verification must happen in a fresh Node process.
+  const result = spawnSync(process.execPath, [scriptPath, CHILD_CHECK_FLAG], {
+    cwd: projectDir,
+    encoding: 'utf8',
+    stdio: ['ignore', 'pipe', 'pipe']
+  })
+
+  return parseChildCheckResult(result)
 }
 
 function runElectronCheck() {
@@ -119,15 +123,33 @@ function runElectronCheck() {
     stdio: ['ignore', 'pipe', 'pipe']
   })
 
+  return parseChildCheckResult(result)
+}
+
+function parseChildCheckResult(result) {
+  const failures = parseCheckFailures(result.stderr)
+
   return {
     ok: result.status === 0,
     status: result.status,
     stdout: result.stdout,
     stderr: result.stderr,
-    error: result.error
+    error: result.error,
+    failures
   }
 }
 
+function parseCheckFailures(stderr) {
+  const failures = []
+  for (const line of (stderr ?? '').split(/\r?\n/)) {
+    const match = /^([^:]+):\s*(.*)$/.exec(line)
+    if (match && NATIVE_MODULES.includes(match[1])) {
+      failures.push({ moduleName: match[1], message: match[2] })
+    }
+  }
+  return failures
+}
+
 function collectNativeModuleFailures() {
   const failures = []
   for (const moduleName of NATIVE_MODULES) {
diff --git a/config/scripts/ensure-native-runtime.test.mjs b/config/scripts/ensure-native-runtime.test.mjs
new file mode 100644
index 000000000..65ba4f0cd
--- /dev/null
+++ b/config/scripts/ensure-native-runtime.test.mjs
@@ -0,0 +1,135 @@
+import { spawnSync } from 'node:child_process'
+import {
+  chmodSync,
+  copyFileSync,
+  mkdirSync,
+  mkdtempSync,
+  readFileSync,
+  rmSync,
+  writeFileSync
+} from 'node:fs'
+import { tmpdir } from 'node:os'
+import { delimiter, join } from 'node:path'
+import { fileURLToPath } from 'node:url'
+import { describe, expect, it } from 'vitest'
+
+const sourceScriptPath = fileURLToPath(new URL('./ensure-native-runtime.mjs', import.meta.url))
+
+describe('ensure-native-runtime', () => {
+  it('rechecks Node native modules in fresh child processes after rebuilding', () => {
+    const projectDir = mkTempProject()
+
+    try {
+      const scriptPath = join(projectDir, 'config', 'scripts', 'ensure-native-runtime.mjs')
+      const logPath = join(projectDir, 'native-runtime.log')
+      const markerPath = join(projectDir, 'rebuilt.marker')
+      const binDir = join(projectDir, 'bin')
+      copyFileSync(sourceScriptPath, scriptPath)
+      writeFakeNativeModules(projectDir)
+      writeFakePnpm(binDir)
+
+      const result = spawnSync(process.execPath, [scriptPath, '--runtime=node'], {
+        cwd: projectDir,
+        encoding: 'utf8',
+        env: envWithPrependedPath(binDir, {
+          ORCA_NATIVE_TEST_LOG: logPath,
+          ORCA_NATIVE_TEST_MARKER: markerPath
+        })
+      })
+
+      expect(result.status, result.stderr).toBe(0)
+      const log = readFileSync(logPath, 'utf8')
+      expect(log).toContain('pnpm rebuild better-sqlite3\n')
+      expect(log.split('\n').filter((line) => line.startsWith('better-sqlite3 '))).toEqual([
+        'better-sqlite3 child marker=false',
+        'better-sqlite3 child marker=true'
+      ])
+    } finally {
+      rmSync(projectDir, { recursive: true, force: true })
+    }
+  })
+})
+
+function mkTempProject() {
+  const projectDir = mkdtempSync(join(tmpdir(), 'orca-native-runtime-'))
+  mkdirSync(join(projectDir, 'config', 'scripts'), { recursive: true })
+  return projectDir
+}
+
+function envWithPrependedPath(binDir, extraEnv) {
+  const pathKey =
+    process.platform === 'win32'
+      ? (Object.keys(process.env).find((key) => key.toLowerCase() === 'path') ?? 'Path')
+      : 'PATH'
+  return {
+    ...process.env,
+    ...extraEnv,
+    [pathKey]: `${binDir}${delimiter}${process.env[pathKey] ?? ''}`
+  }
+}
+
+function writeFakeNativeModules(projectDir) {
+  const sqliteDir = join(projectDir, 'node_modules', 'better-sqlite3')
+  const nodePtyDir = join(projectDir, 'node_modules', 'node-pty')
+  mkdirSync(sqliteDir, { recursive: true })
+  mkdirSync(join(nodePtyDir, 'lib'), { recursive: true })
+
+  writeFileSync(
+    join(sqliteDir, 'index.js'),
+    `
+const { appendFileSync, existsSync } = require('node:fs')
+
+module.exports = class Database {
+  constructor() {
+    const markerExists = existsSync(process.env.ORCA_NATIVE_TEST_MARKER)
+    appendFileSync(
+      process.env.ORCA_NATIVE_TEST_LOG,
+      \`better-sqlite3 \${process.argv.includes('--check-only') ? 'child' : 'parent'} marker=\${markerExists}\\n\`
+    )
+    if (!markerExists) {
+      throw new Error('ABI mismatch sentinel')
+    }
+  }
+
+  close() {}
+}
+`
+  )
+
+  writeFileSync(join(nodePtyDir, 'index.js'), 'module.exports = {}\n')
+  writeFileSync(
+    join(nodePtyDir, 'lib', 'utils.js'),
+    `
+const { appendFileSync } = require('node:fs')
+
+exports.loadNativeModule = function loadNativeModule(nativeName) {
+  appendFileSync(
+    process.env.ORCA_NATIVE_TEST_LOG,
+    \`node-pty \${process.argv.includes('--check-only') ? 'child' : 'parent'} \${nativeName}\\n\`
+  )
+}
+`
+  )
+}
+
+function writeFakePnpm(binDir) {
+  mkdirSync(binDir, { recursive: true })
+  const shimPath = join(binDir, 'pnpm-shim.cjs')
+  writeFileSync(
+    shimPath,
+    `
+const { appendFileSync, writeFileSync } = require('node:fs')
+
+appendFileSync(process.env.ORCA_NATIVE_TEST_LOG, \`pnpm \${process.argv.slice(2).join(' ')}\\n\`)
+writeFileSync(process.env.ORCA_NATIVE_TEST_MARKER, 'rebuilt')
+`
+  )
+
+  const posixPnpmPath = join(binDir, 'pnpm')
+  writeFileSync(posixPnpmPath, `#!/usr/bin/env node\nrequire(${JSON.stringify(shimPath)})\n`)
+  chmodSync(posixPnpmPath, 0o755)
+  writeFileSync(
+    join(binDir, 'pnpm.cmd'),
+    `@echo off\r\n"${process.execPath}" "%~dp0\\pnpm-shim.cjs" %*\r\n`
+  )
+}