diff --git a/src/Commands/core/DeployCommands.php b/src/Commands/core/DeployCommands.php
index c09410f377..fb2273e403 100644
--- a/src/Commands/core/DeployCommands.php
+++ b/src/Commands/core/DeployCommands.php
@@ -9,6 +9,7 @@
 use Consolidation\SiteProcess\ProcessManager;
 use Drush\Attributes as CLI;
 use Drush\Commands\DrushCommands;
+use Drush\Commands\config\ConfigCommands;
 use Drush\Commands\config\ConfigImportCommands;
 use Drush\Commands\core\DeployHookCommands;
 use Drush\Drush;
@@ -25,20 +26,49 @@ final class DeployCommands extends DrushCommands implements SiteAliasManagerAwar
      * Run several commands after performing a code deployment.
      */
     #[CLI\Command(name: self::DEPLOY)]
+    #[CLI\Option(name: 'ignore-mismatched-config', description: 'Proceed with config:import even if changes made by update hooks will be reverted.')]
     #[CLI\Usage(name: 'drush deploy -v -y', description: 'Run updates with verbose logging and accept all prompts.')]
     #[CLI\Version(version: '10.3')]
     #[CLI\Topics(topics: [DocsCommands::DEPLOY])]
     #[CLI\Bootstrap(level: DrupalBootLevels::FULL)]
-    public function deploy(): void
+    public function deploy(array $options = ['ignore-mismatched-config' => false]): void
     {
         $self = $this->siteAliasManager()->getSelf();
         $redispatchOptions = Drush::redispatchOptions();
         $manager = $this->processManager();
 
+        // Prepare custom options for checking configuration state.
+        $configStatusOptions = $redispatchOptions;
+        $configStatusOptions['format'] = 'json';
+        // Record the state of configuration before database updates.
+        $process = $manager->drush($self, ConfigCommands::STATUS, [], $configStatusOptions);
+        $process->mustRun();
+        $originalConfigDiff = $process->getOutputAsJson();
+
         $this->logger()->notice("Database updates start.");
         $process = $manager->drush($self, UpdateDBCommands::UPDATEDB, [], $redispatchOptions);
         $process->mustRun($process->showRealtime());
 
+        // Record the state of configuration after database updates.
+        $process = $manager->drush($self, ConfigCommands::STATUS, [], $configStatusOptions);
+        $process->mustRun();
+        $newConfigDiff = $process->getOutputAsJson();
+
+        // Check for new changes to active configuration that would be lost
+        // during the subsequent configuration import.
+        if ($originalConfigDiff !== $newConfigDiff) {
+            $configDiff = array_diff(
+                array_keys($newConfigDiff),
+                array_keys($originalConfigDiff),
+            );
+            $this->logger()->warning(dt('The following config changes will be lost during config import: :config', [
+                ':config' => implode(', ', $configDiff),
+            ]));
+            if (!$options['ignore-mismatched-config']) {
+                throw new \RuntimeException('Update hooks altered config that is about to be reverted during config import. Use --ignore-mismatched-config to bypass this error. Aborting.');
+            }
+        }
+
         $this->logger()->success("Config import start.");
         $process = $manager->drush($self, ConfigImportCommands::IMPORT, [], $redispatchOptions);
         $process->mustRun($process->showRealtime());