diff --git a/webapi/src/main/resources/application.conf b/webapi/src/main/resources/application.conf
index c53690fe21..3ed032868c 100644
--- a/webapi/src/main/resources/application.conf
+++ b/webapi/src/main/resources/application.conf
@@ -335,12 +335,6 @@ app {
     allow-reload-over-http = false
     allow-reload-over-http = ${?KNORA_WEBAPI_ALLOW_RELOAD_OVER_HTTP}
 
-    // Configuration for updating the repository when Knora is upgraded
-    upgrade {
-        // The directory to which the repository should be downloaded. If not configured, a temporary directory is used.
-        // download-dir = "/tmp/knora-upgrade"
-    }
-
     knora-api {
         // relevant for direct communication inside the knora stack
         internal-host = "0.0.0.0"
diff --git a/webapi/src/main/scala/org/knora/webapi/settings/KnoraSettings.scala b/webapi/src/main/scala/org/knora/webapi/settings/KnoraSettings.scala
index 035cafe402..81884673a5 100644
--- a/webapi/src/main/scala/org/knora/webapi/settings/KnoraSettings.scala
+++ b/webapi/src/main/scala/org/knora/webapi/settings/KnoraSettings.scala
@@ -281,12 +281,6 @@ class KnoraSettingsImpl(config: Config, log: LoggingAdapter) extends Extension {
 
   val prometheusEndpoint: Boolean = config.getBoolean("app.monitoring.prometheus-endpoint")
 
-  val upgradeDownloadDir: Option[String] = if (config.hasPath("app.upgrade.download-dir")) {
-    Some(config.getString("app.upgrade.download-dir"))
-  } else {
-    None
-  }
-
   val shaclShapesDir: Path = Paths.get(config.getString("app.shacl.shapes-dir"))
 
   val featureToggles: Set[FeatureToggleBaseConfig] = if (config.hasPath(featureTogglesPath)) {
diff --git a/webapi/src/main/scala/org/knora/webapi/store/triplestore/upgrade/RepositoryUpdater.scala b/webapi/src/main/scala/org/knora/webapi/store/triplestore/upgrade/RepositoryUpdater.scala
index c350b4b5be..7a9ed5f3da 100644
--- a/webapi/src/main/scala/org/knora/webapi/store/triplestore/upgrade/RepositoryUpdater.scala
+++ b/webapi/src/main/scala/org/knora/webapi/store/triplestore/upgrade/RepositoryUpdater.scala
@@ -1,6 +1,8 @@
 package org.knora.webapi.store.triplestore.upgrade
 
 import java.nio.file.{Files, Path, Paths}
+import java.io.File
+import scala.reflect.io.Directory
 
 import akka.actor.{ActorRef, ActorSystem}
 import akka.http.scaladsl.util.FastFuture
@@ -72,6 +74,24 @@ class RepositoryUpdater(
     log = log
   )
 
+  private val tempDirNamePrefix: String = "knora"
+
+  /**
+    * Deletes directories inside temp directory starting with `tempDirNamePrefix`.
+    */  
+  def deleteTempDirectories(): Unit = {
+    val rootDir = new File("/tmp/")
+    val getTempToDelete = rootDir.listFiles.filter(_.getName.startsWith(tempDirNamePrefix))
+
+    if (getTempToDelete.length != 0) {
+      getTempToDelete.foreach(dir => {
+        val dirToDelete = new Directory(dir)
+        dirToDelete.deleteRecursively()
+      })
+      log.info(s"Deleted temp directories: ${getTempToDelete.map(_.getName()).mkString(", ")}")
+    }
+  }
+
   /**
    * Updates the repository, if necessary, to work with the current version of Knora.
    *
@@ -83,18 +103,20 @@ class RepositoryUpdater(
       requiredRepositoryVersion = org.knora.webapi.KnoraBaseVersion
 
       // Is the repository up to date?
-      repositoryUpToData = foundRepositoryVersion.contains(requiredRepositoryVersion)
+      repositoryUpToDate: Boolean = foundRepositoryVersion.contains(requiredRepositoryVersion)
+
       repositoryUpdatedResponse: RepositoryUpdatedResponse <-
-        if (repositoryUpToData) {
+        if (repositoryUpToDate) {
           // Yes. Nothing more to do.
           FastFuture.successful(RepositoryUpdatedResponse(s"Repository is up to date at $requiredRepositoryVersion"))
         } else {
           // No. Construct the list of updates that it needs.
-
           log.info(
             s"Repository not up-to-date. Found: ${foundRepositoryVersion.getOrElse("None")}, Required: $requiredRepositoryVersion"
           )
 
+          deleteTempDirectories()
+
           val selectedPlugins: Seq[PluginForKnoraBaseVersion] = selectPluginsForNeededUpdates(foundRepositoryVersion)
           log.info(s"Updating repository with transformations: ${selectedPlugins.map(_.versionString).mkString(", ")}")
 
@@ -164,21 +186,8 @@ class RepositoryUpdater(
   private def updateRepositoryWithSelectedPlugins(
     pluginsForNeededUpdates: Seq[PluginForKnoraBaseVersion]
   ): Future[RepositoryUpdatedResponse] = {
-    // Was a download directory specified in the application settings?
-    val downloadDir: Path = settings.upgradeDownloadDir match {
-      case Some(configuredDir) =>
-        // Yes. Use that directory.
-        log.info(s"Repository update using configured download directory $configuredDir")
-        val dirFile = Paths.get(configuredDir)
-        Files.createDirectories(dirFile)
-        dirFile
-
-      case None =>
-        // No. Create a temporary directory.
-        val dirFile = Files.createTempDirectory("knora")
-        log.info(s"Repository update using download directory $dirFile")
-        dirFile
-    }
+    val downloadDir: Path = Files.createTempDirectory(tempDirNamePrefix)
+    log.info(s"Repository update using download directory $downloadDir")
 
     // The file to save the repository in.
     val downloadedRepositoryFile = downloadDir.resolve("downloaded-repository.nq")