diff --git a/app/src/main/java/com/nextcloud/client/database/dao/FileSystemDao.kt b/app/src/main/java/com/nextcloud/client/database/dao/FileSystemDao.kt
index 9d9be7179d3c..16e5db119231 100644
--- a/app/src/main/java/com/nextcloud/client/database/dao/FileSystemDao.kt
+++ b/app/src/main/java/com/nextcloud/client/database/dao/FileSystemDao.kt
@@ -17,6 +17,16 @@ import com.owncloud.android.db.ProviderMeta
 
 @Dao
 interface FileSystemDao {
+    @Query(
+        """
+    SELECT COUNT(*) > 0 FROM ${ProviderMeta.ProviderTableMeta.FILESYSTEM_TABLE_NAME}
+    WHERE ${ProviderMeta.ProviderTableMeta.FILESYSTEM_FILE_LOCAL_PATH} = :localPath
+      AND ${ProviderMeta.ProviderTableMeta.FILESYSTEM_SYNCED_FOLDER_ID} IS NOT NULL
+    LIMIT 1
+"""
+    )
+    suspend fun isBelongToAnyAutoFolder(localPath: String): Boolean
+
     @Insert(onConflict = OnConflictStrategy.REPLACE)
     fun insertOrReplace(filesystemEntity: FilesystemEntity)
 
diff --git a/app/src/main/java/com/nextcloud/client/jobs/BackgroundJobFactory.kt b/app/src/main/java/com/nextcloud/client/jobs/BackgroundJobFactory.kt
index a5a1a7f8ab35..5e573b1c4cd0 100644
--- a/app/src/main/java/com/nextcloud/client/jobs/BackgroundJobFactory.kt
+++ b/app/src/main/java/com/nextcloud/client/jobs/BackgroundJobFactory.kt
@@ -244,6 +244,8 @@ class BackgroundJobFactory @Inject constructor(
             localBroadcastManager.get(),
             backgroundJobManager.get(),
             preferences,
+            FileSystemRepository(dao = database.fileSystemDao(), uploadsStorageManager, context),
+            syncedFolderProvider,
             context,
             params
         )
diff --git a/app/src/main/java/com/nextcloud/client/jobs/autoUpload/FileSystemRepository.kt b/app/src/main/java/com/nextcloud/client/jobs/autoUpload/FileSystemRepository.kt
index 59203b7cc619..671e9b1974d5 100644
--- a/app/src/main/java/com/nextcloud/client/jobs/autoUpload/FileSystemRepository.kt
+++ b/app/src/main/java/com/nextcloud/client/jobs/autoUpload/FileSystemRepository.kt
@@ -35,6 +35,8 @@ class FileSystemRepository(
         const val BATCH_SIZE = 50
     }
 
+    suspend fun isBelongToAnyAutoFolder(localPath: String): Boolean = dao.isBelongToAnyAutoFolder(localPath)
+
     fun deleteAutoUploadAndUploadEntity(syncedFolder: SyncedFolder, localPath: String, entity: FilesystemEntity) {
         Log_OC.d(TAG, "deleting auto upload entity and upload entity")
 
diff --git a/app/src/main/java/com/nextcloud/client/jobs/upload/FileUploadWorker.kt b/app/src/main/java/com/nextcloud/client/jobs/upload/FileUploadWorker.kt
index d2b9b4d7d077..9bf2c366a2dc 100644
--- a/app/src/main/java/com/nextcloud/client/jobs/upload/FileUploadWorker.kt
+++ b/app/src/main/java/com/nextcloud/client/jobs/upload/FileUploadWorker.kt
@@ -19,15 +19,20 @@ import com.nextcloud.client.account.UserAccountManager
 import com.nextcloud.client.device.PowerManagementService
 import com.nextcloud.client.jobs.BackgroundJobManager
 import com.nextcloud.client.jobs.BackgroundJobManagerImpl
+import com.nextcloud.client.jobs.autoUpload.FileSystemRepository
+import com.nextcloud.client.jobs.autoUpload.SyncFolderHelper
 import com.nextcloud.client.jobs.utils.UploadErrorNotificationManager
 import com.nextcloud.client.network.ConnectivityService
 import com.nextcloud.client.preferences.AppPreferences
 import com.nextcloud.utils.ForegroundServiceHelper
 import com.nextcloud.utils.extensions.getPercent
+import com.nextcloud.utils.extensions.toFile
 import com.nextcloud.utils.extensions.updateStatus
 import com.owncloud.android.R
 import com.owncloud.android.datamodel.FileDataStorageManager
 import com.owncloud.android.datamodel.ForegroundServiceType
+import com.owncloud.android.datamodel.SyncedFolder
+import com.owncloud.android.datamodel.SyncedFolderProvider
 import com.owncloud.android.datamodel.ThumbnailsCacheManager
 import com.owncloud.android.datamodel.UploadsStorageManager
 import com.owncloud.android.db.OCUpload
@@ -57,6 +62,8 @@ class FileUploadWorker(
     val localBroadcastManager: LocalBroadcastManager,
     private val backgroundJobManager: BackgroundJobManager,
     val preferences: AppPreferences,
+    val filesystemRepository: FileSystemRepository,
+    val syncedFolderProvider: SyncedFolderProvider,
     val context: Context,
     params: WorkerParameters
 ) : CoroutineWorker(context, params),
@@ -219,10 +226,21 @@ class FileUploadWorker(
         val uploads = uploadsStorageManager.getUploadsByIds(uploadIds, accountName)
         val ocAccount = OwnCloudAccount(user.toPlatformAccount(), context)
         val client = OwnCloudClientManagerFactory.getDefaultSingleton().getClientFor(ocAccount, context)
+        val syncFolderHelper = SyncFolderHelper(context)
+        val syncedFolders = syncedFolderProvider.syncedFolders
 
         for ((index, upload) in uploads.withIndex()) {
             ensureActive()
 
+            if (isBelongToAnySyncedFolder(upload, syncFolderHelper, syncedFolders)) {
+                Log_OC.d(TAG, "skipping upload, will be handled by AutoUploadWorker: ${upload.localPath}")
+                uploadsStorageManager.uploadDao.deleteByRemotePathAndAccountName(
+                    remotePath = upload.remotePath,
+                    accountName = accountName
+                )
+                continue
+            }
+
             if (preferences.isGlobalUploadPaused) {
                 Log_OC.d(TAG, "Upload is paused, skip uploading files!")
                 notificationManager.notifyPaused(
@@ -266,6 +284,20 @@ class FileUploadWorker(
         return@withContext Result.success()
     }
 
+    suspend fun isBelongToAnySyncedFolder(
+        upload: OCUpload,
+        syncFolderHelper: SyncFolderHelper,
+        syncedFolders: List<SyncedFolder>
+    ): Boolean {
+        if (!filesystemRepository.isBelongToAnyAutoFolder(upload.localPath)) return false
+
+        return syncedFolders.any { folder ->
+            val file = upload.localPath.toFile() ?: return false
+            val expectedRemotePath = syncFolderHelper.getAutoUploadRemotePath(folder, file)
+            expectedRemotePath == upload.remotePath
+        }
+    }
+
     private fun sendUploadFinishEvent(
         totalUploadSize: Int,
         currentUploadIndex: Int,