diff --git a/core/Command/Db/CheckSchema.php b/core/Command/Db/CheckSchema.php
index d8f95a5d00051..204bb4f3a7c6a 100644
--- a/core/Command/Db/CheckSchema.php
+++ b/core/Command/Db/CheckSchema.php
@@ -37,18 +37,45 @@ protected function execute(InputInterface $input, OutputInterface $output): int
 		$onlyTable = $input->getArgument('table');
 		$findings = $this->schemaChecker->getFindings($onlyTable);
 
+		$blocking = array_values(array_filter($findings, static fn (array $finding): bool => $finding['enabled']));
+
 		if ($input->getOption('output') === self::OUTPUT_FORMAT_PLAIN) {
 			if ($findings === []) {
 				$output->writeln('<info>The live database schema matches the expected schema.</info>');
 			} else {
-				foreach ($findings as $finding) {
+				foreach ($blocking as $finding) {
 					$output->writeln('<comment>' . $this->schemaChecker->formatFinding($finding) . '</comment>');
 				}
+				$this->printDisabledAppFindings($findings, $output);
 			}
 		} else {
 			$this->writeArrayInOutputFormat($input, $output, $findings);
 		}
 
-		return $findings === [] ? 0 : 1;
+		return $blocking === [] ? 0 : 1;
+	}
+
+	/**
+	 * @param list<array{table: string, type: string, name?: string, changes?: list<string>, app: ?string, enabled: bool}> $findings
+	 */
+	private function printDisabledAppFindings(array $findings, OutputInterface $output): void {
+		$byApp = [];
+		foreach ($findings as $finding) {
+			if (!$finding['enabled']) {
+				$byApp[$finding['app']][] = $finding;
+			}
+		}
+
+		if ($byApp === []) {
+			return;
+		}
+
+		$output->writeln('Disabled apps (not affecting exit code):');
+		foreach ($byApp as $app => $appFindings) {
+			$output->writeln("  {$app}:");
+			foreach ($appFindings as $finding) {
+				$output->writeln('    - <comment>' . $this->schemaChecker->formatFinding($finding) . '</comment>');
+			}
+		}
 	}
 }
diff --git a/core/Command/Upgrade.php b/core/Command/Upgrade.php
index 9fd0f2f8de48a..e706b22a36a91 100644
--- a/core/Command/Upgrade.php
+++ b/core/Command/Upgrade.php
@@ -252,10 +252,26 @@ private function checkSchema(OutputInterface $output): void {
 			return;
 		}
 
-		$output->writeln('<comment>The database schema does not match what is expected for the installed version:</comment>');
+		$byApp = [];
 		foreach ($findings as $finding) {
+			$byApp[$finding['enabled'] ? '' : $finding['app']][] = $finding;
+		}
+
+		$output->writeln('<comment>The database schema does not match what is expected for the installed version:</comment>');
+		foreach ($byApp[''] ?? [] as $finding) {
 			$output->writeln('  - ' . $this->schemaChecker->formatFinding($finding));
 		}
+		unset($byApp['']);
+
+		if ($byApp !== []) {
+			$output->writeln('<comment>Disabled apps:</comment>');
+			foreach ($byApp as $app => $appFindings) {
+				$output->writeln("  {$app}:");
+				foreach ($appFindings as $finding) {
+					$output->writeln('    - ' . $this->schemaChecker->formatFinding($finding));
+				}
+			}
+		}
 		$output->writeln('<comment>Run "occ db:schema:check" for details.</comment>');
 	}
 }
diff --git a/lib/private/DB/SchemaChecker.php b/lib/private/DB/SchemaChecker.php
index 0c6b9d7422f53..7aa6689601cb0 100644
--- a/lib/private/DB/SchemaChecker.php
+++ b/lib/private/DB/SchemaChecker.php
@@ -13,8 +13,11 @@
 use Doctrine\DBAL\Schema\SchemaDiff;
 use Doctrine\DBAL\Schema\TableDiff;
 use Doctrine\DBAL\Types\Types;
+use OC\App\AppManager;
 use OC\Migration\NullOutput;
+use OCP\App\AppPathNotFoundException;
 use OCP\App\IAppManager;
+use OCP\IAppConfig;
 
 /**
  * Compares the live database schema against the schema expected for the
@@ -24,18 +27,21 @@
 class SchemaChecker {
 	public function __construct(
 		private readonly Connection $connection,
+		private readonly IAppConfig $appConfig,
 		private readonly IAppManager $appManager,
 	) {
 	}
 
 	/**
-	 * @return list<array{table: string, type: string, name?: string, changes?: list<string>}>
+	 * @return list<array{table: string, type: string, name?: string, changes?: list<string>, app: ?string, enabled: bool}>
 	 */
 	public function getFindings(?string $onlyTable = null): array {
 		$expectedSchema = new Schema();
-		$this->applyMigrations('core', $expectedSchema);
-		foreach ($this->appManager->getEnabledApps() as $app) {
-			$this->applyMigrations($app, $expectedSchema);
+		$tableOwners = [];
+		$this->applyMigrations('core', $expectedSchema, $tableOwners);
+		// Disabled apps keep their tables, so replay their migrations too.
+		foreach (array_keys($this->appConfig->getAppInstalledVersions()) as $app) {
+			$this->applyMigrations($app, $expectedSchema, $tableOwners);
 		}
 		$this->addMigrationsTable($expectedSchema);
 		$this->materializeUniqueConstraints($expectedSchema);
@@ -50,11 +56,19 @@ public function getFindings(?string $onlyTable = null): array {
 		$comparator = $this->connection->createSchemaManager()->createComparator();
 		$diff = $comparator->compareSchemas($liveSchema, $expectedSchema);
 
-		return $this->buildFindings($diff);
+		$enabledApps = array_flip($this->appManager->getEnabledApps());
+
+		return array_map(function (array $finding) use ($tableOwners, $enabledApps): array {
+			$app = $tableOwners[$finding['table']] ?? null;
+			$finding['app'] = $app;
+			// Only tables owned by a disabled app are non-blocking.
+			$finding['enabled'] = $app === null || $app === 'core' || isset($enabledApps[$app]);
+			return $finding;
+		}, $this->buildFindings($diff));
 	}
 
 	/**
-	 * @param array{table: string, type: string, name?: string, changes?: list<string>} $finding
+	 * @param array{table: string, type: string, name?: string, changes?: list<string>, app?: ?string, enabled?: bool} $finding
 	 */
 	public function formatFinding(array $finding): string {
 		return match ($finding['type']) {
@@ -69,7 +83,28 @@ public function formatFinding(array $finding): string {
 		};
 	}
 
-	private function applyMigrations(string $app, Schema $schema): void {
+	/**
+	 * @param array<string, string> $tableOwners table name => owning app id, updated in place
+	 */
+	private function applyMigrations(string $app, Schema $schema, array &$tableOwners): void {
+		if ($app !== 'core') {
+			try {
+				$appPath = $this->appManager->getAppPath($app);
+			} catch (AppPathNotFoundException) {
+				// Installed, but code is gone: no migrations to replay.
+				return;
+			}
+			// Disabled apps are not autoloaded on boot.
+			/** @var AppManager $appManager */
+			$appManager = $this->appManager;
+			$appManager->registerAutoloading($app, $appPath);
+		}
+
+		$existingTables = [];
+		foreach ($schema->getTables() as $table) {
+			$existingTables[$table->getName()] = true;
+		}
+
 		$output = new NullOutput();
 		$ms = new MigrationService($app, $this->connection, $output);
 		foreach ($ms->getAvailableVersions() as $version) {
@@ -78,6 +113,12 @@ private function applyMigrations(string $app, Schema $schema): void {
 				return new SchemaWrapper($this->connection, $schema);
 			}, []);
 		}
+
+		foreach ($schema->getTables() as $table) {
+			if (!isset($existingTables[$table->getName()])) {
+				$tableOwners[$table->getName()] = $app;
+			}
+		}
 	}
 
 	/**