diff --git a/.github/workflows/database.yaml b/.github/workflows/database.yaml
index e97b8f39..914e7776 100644
--- a/.github/workflows/database.yaml
+++ b/.github/workflows/database.yaml
@@ -102,7 +102,7 @@ jobs:
       - name: Verify existing migrations are not modified or deleted
         run: |
           BASE_REF="${{ steps.base.outputs.base_ref }}"
-          CHANGED=$(git diff --name-only --diff-filter=MD origin/$BASE_REF...HEAD -- migrations/)
+          CHANGED=$(git diff --name-only --diff-filter=MD origin/$BASE_REF...HEAD -- migrations/ | grep -E 'Version[0-9]{14}\.php$' || true)
           if [ -n "$CHANGED" ]; then
             echo "Error: The following existing migrations were modified or deleted:"
             echo "$CHANGED"
@@ -110,6 +110,29 @@ jobs:
           fi
           echo "No existing migrations were modified or deleted."
 
+      - name: Verify new migrations follow naming convention
+        run: |
+          BASE_REF="${{ steps.base.outputs.base_ref }}"
+          NEW_FILES=$(git diff --name-only --diff-filter=A origin/$BASE_REF...HEAD -- migrations/ | grep '\.php$' || true)
+          if [ -z "$NEW_FILES" ]; then
+            echo "No new migrations added."
+            exit 0
+          fi
+
+          FAILED=false
+          for file in $NEW_FILES; do
+            if ! echo "$file" | grep -qE 'Version[0-9]{14}\.php$'; then
+              echo "Error: $file does not follow the migration naming convention (Version{14digits}.php)"
+              FAILED=true
+            else
+              echo "OK: $file"
+            fi
+          done
+
+          if [ "$FAILED" = true ]; then
+            exit 1
+          fi
+
       - name: Verify new migrations have higher version numbers than existing migrations
         run: |
           BASE_REF="${{ steps.base.outputs.base_ref }}"
@@ -128,11 +151,10 @@ jobs:
 
           FAILED=false
           for file in $NEW_MIGRATIONS; do
-            VERSION=$(echo "$file" | grep -oE '[0-9]{14}')
-            if [ -z "$VERSION" ]; then
-              echo "Warning: Could not extract version number from $file"
+            if ! echo "$file" | grep -qE 'Version[0-9]{14}\.php$'; then
               continue
             fi
+            VERSION=$(echo "$file" | grep -oE '[0-9]{14}')
             if [ "$VERSION" -le "$BASE_MAX" ]; then
               echo "Error: $file has version $VERSION which is not higher than the existing maximum $BASE_MAX"
               FAILED=true
diff --git a/docs/configuration-reference.md b/docs/configuration-reference.md
index 039597c1..e7c8118b 100644
--- a/docs/configuration-reference.md
+++ b/docs/configuration-reference.md
@@ -35,6 +35,14 @@ dirigent:
     dev_packages: false
   metadata:
     mirror_vcs_repositories: false
+    retain_pruned_versions:
+      enabled: true
+      tagged_versions: true
+      dev_versions: false
+    retain_stale_revisions:
+      enabled: true
+      tagged_versions: true
+      dev_versions: false
 ```
 
 ## dirigent (root)
@@ -131,6 +139,46 @@ Fetch mirrored packages from their VCS repositories by default when possible.
 
 Sets the fetch strategy of new mirrored packages to **Fetch from VCS**.
 
+### retain_pruned_versions
+
+#### enabled
+
+Type: `boolean` | Default: `true`
+
+Whether to enable or disable retaining pruned versions of packages.
+
+#### tagged_versions
+
+Type: `boolean` | Default: `true`
+
+Retain pruned tagged package versions.
+
+#### dev_versions
+
+Type: `boolean` | Default: `false`
+
+Retain pruned development package versions.
+
+### retain_stale_revisions
+
+#### enabled
+
+Type: `boolean` | Default: `true`
+
+Whether to enable or disable retaining stale revisions of packages.
+
+#### tagged_versions
+
+Type: `boolean` | Default: `true`
+
+Retain stale revisions of tagged package versions.
+
+#### dev_versions
+
+Type: `boolean` | Default: `false`
+
+Retain stale revisions of development package versions.
+
 [iso-8601-durations]: https://en.wikipedia.org/wiki/ISO_8601#Durations
 [symfony]: https://symfony.com
 [symfony-docs-config]: https://symfony.com/doc/current/configuration.html
diff --git a/migrations/AGENTS.md b/migrations/AGENTS.md
new file mode 100644
index 00000000..0398138f
--- /dev/null
+++ b/migrations/AGENTS.md
@@ -0,0 +1,19 @@
+# Agent guidelines for Dirigent development: migrations/
+
+## Generate new migrations
+
+To generate a new migration, execute the `symfony console doctrine:migrations:diff --nowdoc --formatted` command.
+
+## Coding style
+
+- Migration files must follow the naming convention of `Version[0-9]{14}.php`.
+- Migrations must have a non-empty description.
+- Queries should be wrapped in nowdoc by default. Only if a PHP variable is used in the query is it allowed to be wrapped in heredoc.
+
+## Required columns
+
+If a required (non-nullable) column is added to the schema, add it with the following queries:
+
+1. Add a nullable column.
+2. Set a default value for every row in the table.
+3. Remove the nullable flag from the column.
diff --git a/migrations/CLAUDE.md b/migrations/CLAUDE.md
new file mode 100644
index 00000000..d07b8227
--- /dev/null
+++ b/migrations/CLAUDE.md
@@ -0,0 +1,3 @@
+# Agent guidelines for Dirigent development in Claude Code: migrations/
+
+@AGENTS.md
diff --git a/migrations/Version20260416081737.php b/migrations/Version20260416081737.php
new file mode 100644
index 00000000..e61a729a
--- /dev/null
+++ b/migrations/Version20260416081737.php
@@ -0,0 +1,36 @@
+<?php
+
+declare(strict_types=1);
+
+namespace DoctrineMigrations;
+
+use Doctrine\DBAL\Schema\Schema;
+use Doctrine\Migrations\AbstractMigration;
+
+final class Version20260416081737 extends AbstractMigration
+{
+    public function getDescription(): string
+    {
+        return 'Add pruned property to version table';
+    }
+
+    public function up(Schema $schema): void
+    {
+        $this->addSql(<<<'SQL'
+            ALTER TABLE version ADD pruned BOOLEAN DEFAULT NULL
+        SQL);
+        $this->addSql(<<<'SQL'
+            UPDATE version SET pruned = false
+        SQL);
+        $this->addSql(<<<'SQL'
+            ALTER TABLE version ALTER pruned SET NOT NULL
+        SQL);
+    }
+
+    public function down(Schema $schema): void
+    {
+        $this->addSql(<<<'SQL'
+            ALTER TABLE version DROP pruned
+        SQL);
+    }
+}
diff --git a/src/DependencyInjection/DirigentConfiguration.php b/src/DependencyInjection/DirigentConfiguration.php
index af1f62e6..00b6807f 100644
--- a/src/DependencyInjection/DirigentConfiguration.php
+++ b/src/DependencyInjection/DirigentConfiguration.php
@@ -93,6 +93,32 @@ private function addMetadataSection(ArrayNodeDefinition|NodeDefinition $rootNode
                         ->defaultFalse()
                         ->info('Fetch mirrored packages from their VCS repositories by default when possible.')
                     ->end()
+                    ->arrayNode('retain_pruned_versions')
+                        ->canBeDisabled('Retain pruned package versions.')
+                        ->children()
+                            ->booleanNode('tagged_versions')
+                                ->defaultTrue()
+                                ->info('Retain pruned tagged package versions.')
+                            ->end()
+                            ->booleanNode('dev_versions')
+                                ->defaultFalse()
+                                ->info('Retain pruned development package versions.')
+                            ->end()
+                        ->end()
+                    ->end()
+                    ->arrayNode('retain_stale_revisions')
+                        ->canBeDisabled('Retain stale revisions of package versions.')
+                        ->children()
+                            ->booleanNode('tagged_versions')
+                                ->defaultTrue()
+                                ->info('Retain stale revisions of tagged package versions.')
+                            ->end()
+                            ->booleanNode('dev_versions')
+                                ->defaultFalse()
+                                ->info('Retain stale revisions of development package versions.')
+                            ->end()
+                        ->end()
+                    ->end()
                 ->end()
             ->end();
     }
diff --git a/src/DependencyInjection/DirigentExtension.php b/src/DependencyInjection/DirigentExtension.php
index 2332e579..252a782c 100644
--- a/src/DependencyInjection/DirigentExtension.php
+++ b/src/DependencyInjection/DirigentExtension.php
@@ -56,11 +56,31 @@ private function registerEncryptionConfiguration(array $config, ContainerBuilder
     }
 
     /**
-     * @param array{mirror_vcs_repositories: bool} $config
+     * @param array{mirror_vcs_repositories: bool, retain_stale_revisions: array{enabled: bool, tagged_versions: bool, dev_versions: bool}, retain_pruned_versions: array{enabled: bool, tagged_versions: bool, dev_versions: bool}} $config
      */
     private function registerMetadataConfiguration(array $config, ContainerBuilder $container): void
     {
         $container->setParameter('dirigent.metadata.mirror_vcs_repositories', $config['mirror_vcs_repositories']);
+
+        $retainPrunedVersions = $config['retain_pruned_versions']['enabled'];
+        $container->setParameter(
+            name: 'dirigent.metadata.retain_pruned_versions.tagged_versions',
+            value: $retainPrunedVersions && $config['retain_pruned_versions']['tagged_versions'],
+        );
+        $container->setParameter(
+            name: 'dirigent.metadata.retain_pruned_versions.dev_versions',
+            value: $retainPrunedVersions && $config['retain_pruned_versions']['dev_versions'],
+        );
+
+        $retainStaleRevisions = $config['retain_stale_revisions']['enabled'];
+        $container->setParameter(
+            name: 'dirigent.metadata.retain_stale_revisions.tagged_versions',
+            value: $retainStaleRevisions && $config['retain_stale_revisions']['tagged_versions'],
+        );
+        $container->setParameter(
+            name: 'dirigent.metadata.retain_stale_revisions.dev_versions',
+            value: $retainStaleRevisions && $config['retain_stale_revisions']['dev_versions'],
+        );
     }
 
     /**
diff --git a/src/Doctrine/Entity/Version.php b/src/Doctrine/Entity/Version.php
index 85546f54..bb5ec140 100644
--- a/src/Doctrine/Entity/Version.php
+++ b/src/Doctrine/Entity/Version.php
@@ -23,6 +23,9 @@ class Version extends TrackedEntity implements \Stringable
     #[ORM\Column]
     private bool $development;
 
+    #[ORM\Column]
+    private bool $pruned = false;
+
     #[ORM\Column]
     private bool $defaultBranch = false;
 
@@ -91,6 +94,16 @@ public function setDevelopment(bool $development): void
         $this->development = $development;
     }
 
+    public function isPruned(): bool
+    {
+        return $this->pruned;
+    }
+
+    public function setPruned(bool $pruned): void
+    {
+        $this->pruned = $pruned;
+    }
+
     public function isDefaultBranch(): bool
     {
         return $this->defaultBranch;
diff --git a/src/Package/PackageMetadataResolver.php b/src/Package/PackageMetadataResolver.php
index a34cf8ae..de0f9cb8 100644
--- a/src/Package/PackageMetadataResolver.php
+++ b/src/Package/PackageMetadataResolver.php
@@ -23,6 +23,7 @@
 use Composer\Pcre\Preg;
 use Composer\Repository\Vcs\VcsDriverInterface;
 use Doctrine\ORM\EntityManagerInterface;
+use Symfony\Component\DependencyInjection\Attribute\Autowire;
 use Symfony\Component\Messenger\MessageBusInterface;
 use Symfony\Component\Messenger\Stamp\DispatchAfterCurrentBusStamp;
 use Symfony\Component\Messenger\Stamp\TransportNamesStamp;
@@ -36,6 +37,14 @@ public function __construct(
         private KeywordRepository $keywordRepository,
         private RegistryRepository $registryRepository,
         private PackageRepository $packageRepository,
+        #[Autowire(param: 'dirigent.metadata.retain_stale_revisions.tagged_versions')]
+        private bool $retainStaleRevisionsTagged,
+        #[Autowire(param: 'dirigent.metadata.retain_stale_revisions.dev_versions')]
+        private bool $retainStaleRevisionsDev,
+        #[Autowire(param: 'dirigent.metadata.retain_pruned_versions.tagged_versions')]
+        private bool $retainPrunedVersionsTagged,
+        #[Autowire(param: 'dirigent.metadata.retain_pruned_versions.dev_versions')]
+        private bool $retainPrunedVersionsDev,
     ) {
     }
 
@@ -204,7 +213,15 @@ private function updatePackage(Package $package, array $composerPackages, ?VcsDr
 
         // Remove outdated versions
         foreach ($existingVersionMetadata as $version) {
-            $this->entityManager->remove($version);
+            $removeVersion = $version->isDevelopment() ? !$this->retainPrunedVersionsDev : !$this->retainPrunedVersionsTagged;
+            if ($removeVersion) {
+                $this->entityManager->remove($version);
+            } elseif (!$version->isPruned()) {
+                $version->setPruned(true);
+                $version->setUpdatedAt(new \DateTimeImmutable());
+
+                $this->entityManager->persist($version);
+            }
         }
 
         $package->setUpdatedAt(new \DateTimeImmutable());
@@ -214,15 +231,22 @@ private function updatePackage(Package $package, array $composerPackages, ?VcsDr
 
     private function updateVersion(Version $version, CompletePackageInterface $data, ?VcsDriverInterface $driver = null): void
     {
+        $currentMetadata = $version->hasCurrentMetadata() ? $version->getCurrentMetadata() : null;
         $metadata = $this->createMetadata($version, $data, $driver);
 
-        if (!$version->hasCurrentMetadata() || $this->hasMetadataChanged($version->getCurrentMetadata(), $metadata)) {
+        if (null === $currentMetadata || $this->hasMetadataChanged($currentMetadata, $metadata)) {
             $version->setCurrentMetadata($metadata);
 
             $this->entityManager->persist($metadata);
+
+            $removePreviousMetadata = $version->isDevelopment() ? !$this->retainStaleRevisionsDev : !$this->retainStaleRevisionsTagged;
+            if (null !== $currentMetadata && $removePreviousMetadata) {
+                $this->entityManager->remove($currentMetadata);
+            }
         }
 
         $version->setDefaultBranch($data->isDefaultBranch());
+        $version->setPruned(false);
         $version->setUpdatedAt(new \DateTimeImmutable());
 
         $this->entityManager->persist($version);