diff --git a/main/src/main/scala/sbt/internal/Clean.scala b/main/src/main/scala/sbt/internal/Clean.scala
index 9d0094ce3..b6cda9a74 100644
--- a/main/src/main/scala/sbt/internal/Clean.scala
+++ b/main/src/main/scala/sbt/internal/Clean.scala
@@ -226,6 +226,13 @@ private[sbt] object Clean {
           case d: DiskActionCacheStore => d.clear()
           case _                       => ()
         IO.delete(outputDirectory.toFile())
+        IO.delete(
+          s.configuration
+            .provider()
+            .scalaProvider()
+            .launcher()
+            .bootDirectory()
+        )
         s
     Command.command(CleanFull, h)(expunge andThen clearCachesFun)
 }