diff --git a/main/src/main/scala/sbt/internal/Clean.scala b/main/src/main/scala/sbt/internal/Clean.scala
index 9d0094ce3..0d1d9eb96 100644
--- a/main/src/main/scala/sbt/internal/Clean.scala
+++ b/main/src/main/scala/sbt/internal/Clean.scala
@@ -167,10 +167,9 @@ private[sbt] object Clean {
       })
       .flatMapTask { case scope =>
         Def.task {
-          val targetDir = (scope / target).value.toPath
+          val baseDir = (scope / baseDirectory).value.toPath
           val filter = cleanFilter(scope).value
-          // We do not want to inadvertently delete files that are not in the target directory.
-          val excludeFilter: Path => Boolean = path => !path.startsWith(targetDir) || filter(path)
+          val excludeFilter: Path => Boolean = path => !path.startsWith(baseDir) || filter(path)
           val delete = cleanDelete(scope).value
           val st = (scope / streams).value
           taskKey.previous.foreach(_.toSeqPath.foreach(p => if (!excludeFilter(p)) delete(p)))
diff --git a/sbt-app/src/sbt-test/actions/clean-managed-outside-target/build.sbt b/sbt-app/src/sbt-test/actions/clean-managed-outside-target/build.sbt
new file mode 100644
index 000000000..77a169f59
--- /dev/null
+++ b/sbt-app/src/sbt-test/actions/clean-managed-outside-target/build.sbt
@@ -0,0 +1,8 @@
+name := "clean-managed-outside-target"
+scalaVersion := "3.3.1"
+Compile / sourceManaged := baseDirectory.value / "src_managed"
+Compile / sourceGenerators += Def.task {
+  val file = (Compile / sourceManaged).value / "demo" / "Test.scala"
+  IO.write(file, """object Test extends App { println("Hi") }""")
+  Seq(file)
+}.taskValue
diff --git a/sbt-app/src/sbt-test/actions/clean-managed-outside-target/test b/sbt-app/src/sbt-test/actions/clean-managed-outside-target/test
new file mode 100644
index 000000000..b65fdc4db
--- /dev/null
+++ b/sbt-app/src/sbt-test/actions/clean-managed-outside-target/test
@@ -0,0 +1,6 @@
+> compile
+$ exists src_managed/demo/Test.scala
+
+> Compile / managedSourcePaths
+> Compile / managedSourcePaths / clean
+$ absent src_managed/demo/Test.scala