diff --git a/app/workers/certificates.php b/app/workers/certificates.php
index 9f9ce33dbd..1df77f9827 100644
--- a/app/workers/certificates.php
+++ b/app/workers/certificates.php
@@ -98,6 +98,25 @@ class CertificatesV1 extends Worker
             && isset($certificate['issueDate'])
             && (($certificate['issueDate'] + ($expiry)) > \time())
         ) { // Check last issue time
+            
+            // Update document anyway, if needed.
+            // This occurs when a cert is already generated because a different project is using the domain.
+            // By updating here we ensure all domains has certificateId assigned (share same certificate document)
+            if(!isset($document['certificateId'])) {
+                $certificate = new Document($certificate);
+
+                $domain = new Document(\array_merge($document, [
+                    'updated' => \time(),
+                    'certificateId' => $certificate->getId(),
+                ]));
+    
+                $domain = $dbForConsole->updateDocument('domains', $domain->getId(), $domain);
+    
+                if(!$certificate) {
+                    throw new Exception('Failed saving domain to DB');
+                }
+            }
+
             throw new Exception('Renew isn\'t required');
         }
 
diff --git a/app/workers/deletes.php b/app/workers/deletes.php
index 0beb7d01a8..29b9bc5c49 100644
--- a/app/workers/deletes.php
+++ b/app/workers/deletes.php
@@ -41,6 +41,7 @@ class DeletesV1 extends Worker
 
     public function run(): void
     {
+
         $projectId = $this->args['projectId'] ?? '';
         $type = $this->args['type'] ?? '';
 
@@ -530,11 +531,40 @@ class DeletesV1 extends Worker
      */
     protected function deleteCertificates(Document $document): void
     {
+        $consoleDB = $this->getConsoleDB();
+
+        // If domain has certificate generated
+        if(isset($document['certificateId'])) {
+            $domainUsingCertificate = $consoleDB->findOne('domains', [
+                new Query('certificateId', Query::TYPE_EQUAL, [$document['certificateId']])
+            ]);
+
+            if(!$domainUsingCertificate) {
+                $mainDomain = App::getEnv('_APP_DOMAIN_TARGET', '');
+                if($mainDomain === $document->getAttribute('domain')) {
+                    $domainUsingCertificate = $mainDomain;
+                }
+            }
+
+            // If certificate is still used by some domain, mark we can't delete.
+            // Current domain should not be found, because we only have copy. Original domain is already deleted from database.
+            if($domainUsingCertificate) {
+                Console::warning("Skipping certificate deletion, because a domain is still using it.");
+                return;
+            }
+        }
+
         $domain = $document->getAttribute('domain');
         $directory = APP_STORAGE_CERTIFICATES . '/' . $domain;
         $checkTraversal = realpath($directory) === $directory;
 
         if ($domain && $checkTraversal && is_dir($directory)) {
+            // Delete certificate document, so Appwrite is aware of change
+            if(isset($document['certificateId'])) {
+                $consoleDB->deleteDocument('certificates', $document['certificateId']);
+            }
+
+            // Delete files, so Traefik is aware of change
             array_map('unlink', glob($directory . '/*.*'));
             rmdir($directory);
             Console::info("Deleted certificate files for {$domain}");