diff --git a/build/spl-autoload-functions-php-8.neon b/build/spl-autoload-functions-php-8.neon
index 36693218894..ee64febde20 100644
--- a/build/spl-autoload-functions-php-8.neon
+++ b/build/spl-autoload-functions-php-8.neon
@@ -2,5 +2,9 @@ parameters:
 	ignoreErrors:
 		-
 			message: "#^PHPDoc tag @var with type list\\<callable\\(string\\): void\\>\\|false is not subtype of native type list\\<callable\\(string\\): void\\>\\.$#"
-			count: 2
+			count: 1
 			path: ../src/Command/CommandHelper.php
+		-
+			message: "#^PHPDoc tag @var with type list\\<callable\\(string\\): void\\>\\|false is not subtype of native type list\\<callable\\(string\\): void\\>\\.$#"
+			count: 2
+			path: ../src/Command/BootstrapFilesRunner.php
diff --git a/src/Command/AnalyseApplication.php b/src/Command/AnalyseApplication.php
index 7ec2169d4fb..1f437b604d0 100644
--- a/src/Command/AnalyseApplication.php
+++ b/src/Command/AnalyseApplication.php
@@ -37,6 +37,7 @@ final class AnalyseApplication
 {
 
 	public function __construct(
+		private BootstrapFilesRunner $bootstrapFilesRunner,
 		private AnalyserRunner $analyserRunner,
 		private AnalyserResultFinalizer $analyserResultFinalizer,
 		private StubValidator $stubValidator,
@@ -50,6 +51,7 @@ public function __construct(
 	/**
 	 * @param string[] $files
 	 * @param mixed[]|null $projectConfigArray
+	 * @throws InceptionNotSuccessfulException
 	 */
 	public function analyse(
 		array $files,
@@ -214,6 +216,7 @@ private function mapCollectedData(array $collectedData): array
 	/**
 	 * @param string[] $files
 	 * @param string[] $allAnalysedFiles
+	 * @throws InceptionNotSuccessfulException
 	 */
 	private function runAnalyser(
 		array $files,
@@ -230,6 +233,11 @@ private function runAnalyser(
 		$filesCount = count($files);
 		$allAnalysedFilesCount = count($allAnalysedFiles);
 		if ($filesCount === 0) {
+			// nothing to analyse, but the deferred bootstrapFiles still must
+			// run in the main thread: the phases that follow may reflect
+			// analysed code (stub validation, collector rules from the result
+			// cache)
+			$this->bootstrapFilesRunner->run($errorOutput, $debug);
 			$errorOutput->getStyle()->progressStart($allAnalysedFilesCount);
 			$errorOutput->getStyle()->progressAdvance($allAnalysedFilesCount);
 			$errorOutput->getStyle()->progressFinish();
@@ -296,7 +304,7 @@ private function runAnalyser(
 			}
 		}
 
-		$analyserResult = $this->analyserRunner->runAnalyser($files, $allAnalysedFiles, $preFileCallback, $postFileCallback, $debug, true, $projectConfigFile, $tmpFile, $insteadOfFile, $input);
+		$analyserResult = $this->analyserRunner->runAnalyser($files, $allAnalysedFiles, $preFileCallback, $postFileCallback, $debug, true, $projectConfigFile, $tmpFile, $insteadOfFile, $input, $errorOutput);
 
 		if (!$debug) {
 			$errorOutput->getStyle()->progressFinish();
diff --git a/src/Command/AnalyseCommand.php b/src/Command/AnalyseCommand.php
index bd073559b80..d822af5a370 100644
--- a/src/Command/AnalyseCommand.php
+++ b/src/Command/AnalyseCommand.php
@@ -201,6 +201,7 @@ protected function execute(InputInterface $input, OutputInterface $output): int
 				$tmpFile,
 				$insteadOfFile,
 				true,
+				deferBootstrapFiles: true,
 			);
 		} catch (InceptionNotSuccessfulException $e) {
 			return 1;
diff --git a/src/Command/AnalyserRunner.php b/src/Command/AnalyserRunner.php
index dac67670a14..be77e56245c 100644
--- a/src/Command/AnalyserRunner.php
+++ b/src/Command/AnalyserRunner.php
@@ -30,6 +30,7 @@ public function __construct(
 		private Analyser $analyser,
 		private ParallelAnalyser $parallelAnalyser,
 		private CpuCoreCounter $cpuCoreCounter,
+		private BootstrapFilesRunner $bootstrapFilesRunner,
 	)
 	{
 	}
@@ -39,6 +40,7 @@ public function __construct(
 	 * @param string[] $allAnalysedFiles
 	 * @param Closure(string $file): void|null $preFileCallback
 	 * @param Closure(int, list<string>=): void|null $postFileCallback
+	 * @throws InceptionNotSuccessfulException
 	 */
 	public function runAnalyser(
 		array $files,
@@ -51,6 +53,7 @@ public function runAnalyser(
 		?string $tmpFile,
 		?string $insteadOfFile,
 		InputInterface $input,
+		Output $errorOutput,
 	): AnalyserResult
 	{
 		$filesCount = count($files);
@@ -93,10 +96,22 @@ public function runAnalyser(
 				if ($result === null) {
 					throw new ShouldNotHappenException();
 				}
+				// the parallel analysis is over and no more workers fork - the
+				// main thread runs the deferred bootstrapFiles now, before the
+				// phases that may reflect analysed code (stub validation,
+				// collector rules)
+				$this->bootstrapFilesRunner->run($errorOutput, $debug);
+
 				return $result;
 			}
 		}
 
+		// every path below analyses in-process - including the fall-throughs
+		// from the parallel branch above (no main script, zero-process
+		// schedule) - so the main thread runs the deferred bootstrapFiles
+		// first
+		$this->bootstrapFilesRunner->run($errorOutput, $debug);
+
 		return $this->analyser->analyse(
 			$this->switchTmpFile($files, $insteadOfFile, $tmpFile),
 			$preFileCallback,
diff --git a/src/Command/BootstrapFilesRunner.php b/src/Command/BootstrapFilesRunner.php
new file mode 100644
index 00000000000..a0df68c46ce
--- /dev/null
+++ b/src/Command/BootstrapFilesRunner.php
@@ -0,0 +1,88 @@
+<?php declare(strict_types = 1);
+
+namespace PHPStan\Command;
+
+use PHPStan\DependencyInjection\AutowiredService;
+use PHPStan\DependencyInjection\Container;
+use function array_merge;
+use function PHPStan\collectNewAutoloadFunctions;
+use function spl_autoload_functions;
+
+/**
+ * Executes the configured bootstrapFiles, once per process.
+ *
+ * The analyse flow calls run() at exactly the places that need the files
+ * executed - resources they open (an objectManagerLoader's database
+ * connection, a query reflector's PDO) must not be inherited by forked
+ * children:
+ *
+ * - the main thread right before an in-process analysis (AnalyserRunner),
+ * - every worker, spawned or forked (WorkerRunner),
+ * - the main thread after the workers of a parallel analysis
+ *   (AnalyserRunner), and after a fully cached run (AnalyseApplication) -
+ *   before the phases that may reflect analysed code.
+ *
+ * Every other command runs them eagerly in CommandHelper::begin(). The
+ * once-per-process latch exists for a worker forked from a parent that
+ * already ran the files (the fixer flow runs them eagerly before its
+ * repeated analysis rounds): such a worker inherits that execution and
+ * run() must not repeat it.
+ */
+#[AutowiredService]
+final class BootstrapFilesRunner
+{
+
+	private bool $hasRun = false;
+
+	public function __construct(private Container $container)
+	{
+	}
+
+	/**
+	 * @throws InceptionNotSuccessfulException
+	 */
+	public function run(Output $errorOutput, bool $debugEnabled): void
+	{
+		if ($this->hasRun) {
+			return;
+		}
+		$this->hasRun = true;
+
+		/** @var list<callable(string): void>|false $autoloadFunctionsBefore */
+		$autoloadFunctionsBefore = spl_autoload_functions();
+
+		foreach ($this->container->getParameter('bootstrapFiles') as $bootstrapFile) {
+			CommandHelper::executeBootstrapFile($bootstrapFile, $this->container, $errorOutput, $debugEnabled);
+		}
+
+		self::mergeNewAutoloadFunctions($autoloadFunctionsBefore);
+	}
+
+	/**
+	 * Merges autoloaders registered since $autoloadFunctionsBefore into the
+	 * globals the BetterReflection source locators consult lazily (see
+	 * autoloadFunctions.php) - late merging in a deferred or forked run is
+	 * picked up by the next reflection ask.
+	 *
+	 * @param list<callable(string): void>|false $autoloadFunctionsBefore
+	 */
+	public static function mergeNewAutoloadFunctions(array|false $autoloadFunctionsBefore): void
+	{
+		/** @var list<callable(string): void>|false $autoloadFunctionsAfter */
+		$autoloadFunctionsAfter = spl_autoload_functions();
+		if ($autoloadFunctionsBefore === false || $autoloadFunctionsAfter === false) {
+			return;
+		}
+
+		$collectedAutoloadFunctions = collectNewAutoloadFunctions($autoloadFunctionsBefore, $autoloadFunctionsAfter);
+		$GLOBALS['__phpstanAutoloadFunctions'] = array_merge(
+			$GLOBALS['__phpstanAutoloadFunctions'] ?? [],
+			$collectedAutoloadFunctions['appended'],
+		);
+		$GLOBALS['__phpstanAutoloadFunctionsPrependedToComposer'] = array_merge(
+			$GLOBALS['__phpstanAutoloadFunctionsPrependedToComposer'] ?? [],
+			$collectedAutoloadFunctions['prepended'],
+		);
+	}
+
+}
diff --git a/src/Command/CommandHelper.php b/src/Command/CommandHelper.php
index 30cd4561dd2..4039d257a5e 100644
--- a/src/Command/CommandHelper.php
+++ b/src/Command/CommandHelper.php
@@ -41,7 +41,6 @@
 use function array_filter;
 use function array_key_exists;
 use function array_map;
-use function array_merge;
 use function array_values;
 use function class_exists;
 use function count;
@@ -57,7 +56,6 @@
 use function is_file;
 use function is_readable;
 use function is_string;
-use function PHPStan\collectNewAutoloadFunctions;
 use function register_shutdown_function;
 use function spl_autoload_functions;
 use function sprintf;
@@ -96,6 +94,7 @@ public static function begin(
 		?string $singleReflectionFile,
 		?string $singleReflectionInsteadOfFile,
 		bool $cleanupContainerCache,
+		bool $deferBootstrapFiles = false,
 	): InceptionResult
 	{
 		$stdOutput = new SymfonyOutput($output, new SymfonyStyle(new ErrorsConsoleStyle($input, $output)));
@@ -520,23 +519,25 @@ public static function begin(
 			$defaultLevelUsed = false;
 		}
 
-		foreach ($container->getParameter('bootstrapFiles') as $bootstrapFileFromArray) {
-			self::executeBootstrapFile($bootstrapFileFromArray, $container, $errorOutput, $debugEnabled);
-		}
-
-		/** @var list<callable(string): void>|false $autoloadFunctionsAfter */
-		$autoloadFunctionsAfter = spl_autoload_functions();
-
-		if ($autoloadFunctionsBefore !== false && $autoloadFunctionsAfter !== false) {
-			$collectedAutoloadFunctions = collectNewAutoloadFunctions($autoloadFunctionsBefore, $autoloadFunctionsAfter);
-			$GLOBALS['__phpstanAutoloadFunctions'] = array_merge(
-				$GLOBALS['__phpstanAutoloadFunctions'] ?? [],
-				$collectedAutoloadFunctions['appended'],
-			);
-			$GLOBALS['__phpstanAutoloadFunctionsPrependedToComposer'] = array_merge(
-				$GLOBALS['__phpstanAutoloadFunctionsPrependedToComposer'] ?? [],
-				$collectedAutoloadFunctions['prepended'],
-			);
+		// merges autoloaders registered since the top of begin() - the
+		// --autoload-file require, anything container creation pulled in. This
+		// cannot wait for the bootstrapFiles run: when that run is deferred,
+		// the parent analyses long before it happens, and the source locators
+		// must see these autoloaders throughout. It also cannot fold into
+		// BootstrapFilesRunner::run() - by the time run() snapshots its own
+		// before-list these are already registered, so its diff would exclude
+		// them. run() brackets only the bootstrap files themselves, in
+		// whichever process executes them.
+		BootstrapFilesRunner::mergeNewAutoloadFunctions($autoloadFunctionsBefore);
+
+		// the analyse flow defers bootstrapFiles to the exact places that need
+		// them: the main thread right before an in-process analysis, every
+		// worker (spawned or forked - WorkerRunner), and the main thread after
+		// the workers of a parallel analysis (AnalyserRunner) - resources the
+		// files open (database connections!) must not be inherited by forked
+		// children. Every other command runs them here.
+		if (!$deferBootstrapFiles) {
+			$container->getByType(BootstrapFilesRunner::class)->run($errorOutput, $debugEnabled);
 		}
 
 		if (PHP_VERSION_ID >= 80000) {
@@ -627,7 +628,7 @@ public static function begin(
 	/**
 	 * @throws InceptionNotSuccessfulException
 	 */
-	private static function executeBootstrapFile(
+	public static function executeBootstrapFile(
 		string $file,
 		Container $container,
 		Output $errorOutput,
diff --git a/src/Command/WorkerCommand.php b/src/Command/WorkerCommand.php
index c8be288469e..5199808d7b0 100644
--- a/src/Command/WorkerCommand.php
+++ b/src/Command/WorkerCommand.php
@@ -100,6 +100,7 @@ protected function execute(InputInterface $input, OutputInterface $output): int
 				$tmpFile,
 				$insteadOfFile,
 				false,
+				deferBootstrapFiles: true,
 			);
 		} catch (InceptionNotSuccessfulException $e) {
 			return 1;
@@ -143,14 +144,19 @@ protected function execute(InputInterface $input, OutputInterface $output): int
 		// child can reuse it without re-booting (see ParallelAnalyser).
 		$workerRunner = $container->getByType(WorkerRunner::class);
 
-		return $workerRunner->run(
-			$output,
-			$analysedFiles,
-			(int) $port,
-			$identifier,
-			$tmpFile,
-			$insteadOfFile,
-		);
+		try {
+			return $workerRunner->run(
+				$output,
+				$analysedFiles,
+				(int) $port,
+				$identifier,
+				$tmpFile,
+				$insteadOfFile,
+			);
+		} catch (InceptionNotSuccessfulException) {
+			// a deferred bootstrap file failed - its error is already printed
+			return 1;
+		}
 	}
 
 }
diff --git a/src/Parallel/ForkedProcess.php b/src/Parallel/ForkedProcess.php
index 0d26422d29f..caf6d958108 100644
--- a/src/Parallel/ForkedProcess.php
+++ b/src/Parallel/ForkedProcess.php
@@ -2,6 +2,7 @@
 
 namespace PHPStan\Parallel;
 
+use PHPStan\Command\InceptionNotSuccessfulException;
 use PHPStan\ShouldNotHappenException;
 use React\EventLoop\LoopInterface;
 use React\EventLoop\TimerInterface;
@@ -88,14 +89,20 @@ public function start(callable $onData, callable $onError, callable $onExit): vo
 			// the worker on its own fresh event loop and never return.
 			$this->server->close();
 			$output = new StreamOutput($this->stdOut);
-			$exitCode = $this->workerRunner->run(
-				$output,
-				$this->analysedFiles,
-				$this->serverPort,
-				$this->identifier,
-				$this->tmpFile,
-				$this->insteadOfFile,
-			);
+			try {
+				$exitCode = $this->workerRunner->run(
+					$output,
+					$this->analysedFiles,
+					$this->serverPort,
+					$this->identifier,
+					$this->tmpFile,
+					$this->insteadOfFile,
+				);
+			} catch (InceptionNotSuccessfulException) {
+				// a deferred bootstrap file failed - its error is already
+				// printed to the child's collected stdout
+				exit(1);
+			}
 			exit($exitCode);
 		}
 
diff --git a/src/Parallel/WorkerRunner.php b/src/Parallel/WorkerRunner.php
index c570454e7f9..ae14e2d4c56 100644
--- a/src/Parallel/WorkerRunner.php
+++ b/src/Parallel/WorkerRunner.php
@@ -8,6 +8,11 @@
 use PHPStan\Analyser\InternalError;
 use PHPStan\Analyser\NodeScopeResolver;
 use PHPStan\Collectors\Registry as CollectorRegistry;
+use PHPStan\Command\BootstrapFilesRunner;
+use PHPStan\Command\ErrorsConsoleStyle;
+use PHPStan\Command\InceptionNotSuccessfulException;
+use PHPStan\Command\Symfony\SymfonyOutput;
+use PHPStan\Command\Symfony\SymfonyStyle;
 use PHPStan\DependencyInjection\AutowiredParameter;
 use PHPStan\DependencyInjection\AutowiredService;
 use PHPStan\Rules\Registry as RuleRegistry;
@@ -16,6 +21,7 @@
 use React\Socket\TcpConnector;
 use React\Stream\ReadableStreamInterface;
 use React\Stream\WritableStreamInterface;
+use Symfony\Component\Console\Input\StringInput;
 use Symfony\Component\Console\Output\OutputInterface;
 use Throwable;
 use function array_fill_keys;
@@ -43,6 +49,7 @@ final class WorkerRunner
 {
 
 	public function __construct(
+		private BootstrapFilesRunner $bootstrapFilesRunner,
 		private FileAnalyser $fileAnalyser,
 		private RuleRegistry $ruleRegistry,
 		private CollectorRegistry $collectorRegistry,
@@ -56,6 +63,7 @@ public function __construct(
 	/**
 	 * @param string[] $analysedFiles the full analysed-files list (raw, before tmp-file substitution)
 	 * @return int exit code (0 on success, 1 if a worker-communication error occurred)
+	 * @throws InceptionNotSuccessfulException
 	 */
 	public function run(
 		OutputInterface $output,
@@ -66,6 +74,16 @@ public function run(
 		?string $insteadOfFile,
 	): int
 	{
+		// every worker - spawned or forked - runs the bootstrapFiles itself,
+		// so resources they open (database connections!) are per-worker. The
+		// one exception is a worker forked from a parent that already ran
+		// them (the fixer flow runs them eagerly): it inherits that execution
+		// and the once-per-process latch skips
+		$this->bootstrapFilesRunner->run(
+			new SymfonyOutput($output, new SymfonyStyle(new ErrorsConsoleStyle(new StringInput(''), $output))),
+			false,
+		);
+
 		$analysedFiles = $this->switchTmpFile($analysedFiles, $insteadOfFile, $tmpFile);
 		$this->nodeScopeResolver->setAnalysedFiles($analysedFiles);
 		$analysedFiles = array_fill_keys($analysedFiles, true);
diff --git a/tests/PHPStan/Command/AnalyseApplicationIntegrationTest.php b/tests/PHPStan/Command/AnalyseApplicationIntegrationTest.php
index f7d7b086f39..41303eafbfa 100644
--- a/tests/PHPStan/Command/AnalyseApplicationIntegrationTest.php
+++ b/tests/PHPStan/Command/AnalyseApplicationIntegrationTest.php
@@ -78,19 +78,23 @@ private function runPath(string $path, int $expectedStatusCode): string
 			null,
 			CommandHelper::DEFAULT_LEVEL,
 		);
-		$analysisResult = $analyserApplication->analyse(
-			[$path],
-			true,
-			$symfonyOutput,
-			$symfonyOutput,
-			false,
-			true,
-			null,
-			null,
-			null,
-			null,
-			$this->createStub(InputInterface::class),
-		);
+		try {
+			$analysisResult = $analyserApplication->analyse(
+				[$path],
+				true,
+				$symfonyOutput,
+				$symfonyOutput,
+				false,
+				true,
+				null,
+				null,
+				null,
+				null,
+				$this->createStub(InputInterface::class),
+			);
+		} catch (InceptionNotSuccessfulException) {
+			$this->fail('Inception was not successful.');
+		}
 		$statusCode = $errorFormatter->formatErrors($analysisResult, $symfonyOutput);
 
 		rewind($output->getStream());