diff --git a/main/src/main/scala/sbt/Defaults.scala b/main/src/main/scala/sbt/Defaults.scala
index cac5e7338..f2646f50a 100755
--- a/main/src/main/scala/sbt/Defaults.scala
+++ b/main/src/main/scala/sbt/Defaults.scala
@@ -256,9 +256,9 @@ object Defaults extends BuildCommon {
       skip :== false,
       taskTemporaryDirectory := { val dir = IO.createTemporaryDirectory; dir.deleteOnExit(); dir },
       onComplete := {
-        val dir = taskTemporaryDirectory.value;
+        val tempDirectory = taskTemporaryDirectory.value
         () =>
-          { IO.delete(dir); IO.createDirectory(dir) }
+          Clean.deleteContents(tempDirectory, _ => false)
       },
       useSuperShell :== sbt.internal.TaskProgress.isEnabled,
       progressReports := { (s: State) =>
diff --git a/main/src/main/scala/sbt/internal/Clean.scala b/main/src/main/scala/sbt/internal/Clean.scala
index f66323e74..83629d505 100644
--- a/main/src/main/scala/sbt/internal/Clean.scala
+++ b/main/src/main/scala/sbt/internal/Clean.scala
@@ -14,12 +14,31 @@ import java.nio.file.{ DirectoryNotEmptyException, Files }
 import sbt.Def._
 import sbt.Keys._
 import sbt.Project.richInitializeTask
-import sbt.internal.GlobLister._
-import sbt.io.AllPassFilter
 import sbt.io.syntax._
+import sbt.io.{ AllPassFilter, FileTreeView, TypedPath }
+import sbt.util.Level
 
 object Clean {
 
+  def deleteContents(file: File, exclude: TypedPath => Boolean): Unit =
+    deleteContents(file, exclude, FileTreeView.DEFAULT, tryDelete((_: String) => {}))
+  def deleteContents(
+      file: File,
+      exclude: TypedPath => Boolean,
+      view: FileTreeView,
+      delete: File => Unit
+  ): Unit = {
+    def deleteRecursive(file: File): Unit = {
+      view.list(file * AllPassFilter).filterNot(exclude).foreach {
+        case dir if dir.isDirectory =>
+          deleteRecursive(dir.toPath.toFile)
+          delete(dir.toPath.toFile)
+        case f => delete(f.toPath.toFile)
+      }
+    }
+    deleteRecursive(file)
+  }
+
   /**
    * Provides an implementation for the clean task. It delegates to [[taskIn]] using the
    * resolvedScoped key to set the scope.
@@ -41,22 +60,37 @@ object Clean {
         case f if f.isDirectory => f * AllPassFilter
         case f                  => f.toGlob
       } ++ cleanKeepGlobs.value
-      val excludeFilter: File => Boolean = excludes.toFileFilter.accept
-      val globDeletions = (outputs in scope).value.unique.filterNot(excludeFilter)
-      val toDelete = cleanFiles.value.filterNot(excludeFilter) match {
-        case f @ Seq(_, _*) => (globDeletions ++ f).distinct
-        case _              => globDeletions
+      val excludeFilter: TypedPath => Boolean = excludes.toTypedPathFilter
+      val debug = (logLevel in scope).?.value.orElse(state.value.get(logLevel.key)) match {
+        case Some(Level.Debug) =>
+          (string: String) =>
+            println(s"[debug] $string")
+        case _ =>
+          (_: String) =>
+            {}
       }
-      val logger = streams.value.log
-      toDelete.sorted.reverseIterator.foreach { f =>
-        logger.debug(s"clean -- deleting file $f")
-        try Files.deleteIfExists(f.toPath)
-        catch {
-          case _: DirectoryNotEmptyException =>
-            logger.debug(s"clean -- unable to delete non-empty directory $f")
-          case e: IOException =>
-            logger.debug(s"Caught unexpected exception $e deleting $f")
+      val delete = tryDelete(debug)
+      cleanFiles.value.sorted.reverseIterator.foreach(delete)
+      (outputs in scope).value.foreach { g =>
+        val filter: TypedPath => Boolean = {
+          val globFilter = g.toTypedPathFilter
+          tp =>
+            !globFilter(tp) || excludeFilter(tp)
         }
+        deleteContents(g.base.toFile, filter, FileTreeView.DEFAULT, delete)
+        delete(g.base.toFile)
       }
     } tag Tags.Clean
+  private def tryDelete(debug: String => Unit): File => Unit = file => {
+    try {
+      debug(s"clean -- deleting file $file")
+      Files.deleteIfExists(file.toPath)
+      ()
+    } catch {
+      case _: DirectoryNotEmptyException =>
+        debug(s"clean -- unable to delete non-empty directory $file")
+      case e: IOException =>
+        debug(s"Caught unexpected exception $e deleting $file")
+    }
+  }
 }