diff --git a/lib/BackgroundJobs/IndexerJob.php b/lib/BackgroundJobs/IndexerJob.php
index cd1c00ca..58a24a53 100644
--- a/lib/BackgroundJobs/IndexerJob.php
+++ b/lib/BackgroundJobs/IndexerJob.php
@@ -47,6 +47,7 @@ class IndexerJob extends TimedJob {
 
 	public const DEFAULT_JOB_INTERVAL = 30 * 60;
 	public const DEFAULT_MAX_INDEXING_TIME = 30 * 60;
+	private const INDEX_COMPLETION_THRESHOLD = 0.02; // 2%
 
 	// Assuming a backend capacity of 50 files per minute we can send 1500 files in half an hour
 	// Specifying a higher number here will still be overruled by the max indexing time
@@ -325,15 +326,21 @@ private function setInitialIndexCompletion(): void {
 		}
 		try {
 			$queuedNewFilesCount = $this->queue->countNewFiles();
+			$eligibleFilesCount = $this->storageService->countFiles();
+			// if the new files in the queue are less than 2% of the total eligible files, we consider the
+			// initial indexing complete this allows for some margin of error in case some files were
+			// added while we were indexing but still ensures that we have indexed the vast majority of
+			// files at least once
+			$thresholdCount = (float)$eligibleFilesCount * self::INDEX_COMPLETION_THRESHOLD;
 		} catch (\OCP\DB\Exception $e) {
-			$this->logger->warning('Could not count queued new files', ['exception' => $e]);
+			$this->logger->warning('Could not count queued new files or total eligible files', ['exception' => $e]);
 			return;
 		}
 		$crawlJobCount = $this->getJobCount(StorageCrawlJob::class);
 
 		// if any storage crawler jobs are still running or there are still new files in the queue,
 		// we are still indexing files that were never indexed before.
-		if ($crawlJobCount > 0 || $queuedNewFilesCount > 0) {
+		if ($crawlJobCount > 0 || $queuedNewFilesCount > $thresholdCount) {
 			return;
 		}
 
diff --git a/lib/Service/StorageService.php b/lib/Service/StorageService.php
index fbc1aaab..b9372591 100644
--- a/lib/Service/StorageService.php
+++ b/lib/Service/StorageService.php
@@ -13,12 +13,11 @@
 use OC\Files\Cache\CacheQueryBuilder;
 use OCA\ContextChat\AppInfo\Application;
 use OCA\ContextChat\Logger;
-use OCP\DB\Exception;
+use OCP\DB\Exception as DBException;
 use OCP\DB\QueryBuilder\IQueryBuilder;
 use OCP\Files\Cache\IFileAccess;
 use OCP\Files\Config\ICachedMountInfo;
 use OCP\Files\Config\IUserMountCache;
-use OCP\Files\File;
 use OCP\Files\Folder;
 use OCP\Files\IMimeTypeLoader;
 use OCP\Files\IRootFolder;
@@ -51,7 +50,7 @@ public function __construct(
 	}
 
 	/**
-	 * @throws Exception
+	 * @throws DBException
 	 */
 	public function countFiles(): int {
 		$totalCount = 0;
@@ -75,7 +74,7 @@ public function countFilesInMount(int $storageId, int $rootId): int {
 			/** @var array{path:string}|false $root */
 			$root = $result->fetch();
 			$result->closeCursor();
-		} catch (Exception $e) {
+		} catch (DBException $e) {
 			$this->logger->error('Could not fetch storage root', ['exception' => $e]);
 			return 0;
 		}
@@ -115,7 +114,7 @@ public function countFilesInMount(int $storageId, int $rootId): int {
 				->andWhere($qb->expr()->lte('filecache.size', $qb->createNamedParameter(Application::CC_MAX_SIZE, IQueryBuilder::PARAM_INT)))
 				->andWhere($qb->expr()->gt('filecache.size', $qb->createNamedParameter(0, IQueryBuilder::PARAM_INT)));
 			$result = $qb->executeQuery();
-		} catch (Exception $e) {
+		} catch (DBException $e) {
 			$this->logger->error('Could not count files in mount: storage=' . $storageId . ' root=' . $rootId, ['exception' => $e]);
 			return 0;
 		}
@@ -136,7 +135,7 @@ private function isFileAccessAvailable(): bool {
 
 	/**
 	 * @return \Generator<array{root_id: int, overridden_root: int, storage_id: int}>
-	 * @throws \OCP\DB\Exception
+	 * @throws DBException
 	 */
 	public function getMounts(): \Generator {
 		if (!$this->isFileAccessAvailable()) {
@@ -148,7 +147,7 @@ public function getMounts(): \Generator {
 
 	/**
 	 * @return \Generator<array{root_id: int, overridden_root: int, storage_id: int}>
-	 * @throws \OCP\DB\Exception
+	 * @throws DBException
 	 */
 	private function getMountsOld(): \Generator {
 		$qb = $this->db->getQueryBuilder();
@@ -181,7 +180,7 @@ private function getMountsOld(): \Generator {
 					if ($root !== false) {
 						$overrideRoot = (int)$root['fileid'];
 					}
-				} catch (Exception $e) {
+				} catch (DBException $e) {
 					$this->logger->error('Could not fetch home storage files root for storage ' . $storageId, ['exception' => $e]);
 					continue;
 				}
@@ -240,7 +239,7 @@ private function getFilesInMountOld(int $storageId, int $rootId, int $lastFileId
 			/** @var array{path:string}|false $root */
 			$root = $result->fetch();
 			$result->closeCursor();
-		} catch (Exception $e) {
+		} catch (DBException $e) {
 			$this->logger->error('Could not fetch storage root', ['exception' => $e]);
 			return;
 		}
@@ -280,7 +279,7 @@ private function getFilesInMountOld(int $storageId, int $rootId, int $lastFileId
 			}
 			$files = $qb->orderBy('filecache.fileid', 'ASC')
 				->executeQuery();
-		} catch (Exception $e) {
+		} catch (DBException $e) {
 			$this->logger->error('Could not fetch files', ['exception' => $e]);
 			return;
 		}