diff --git a/main/src/main/scala/sbt/Defaults.scala b/main/src/main/scala/sbt/Defaults.scala
index 888d42cdb..1273a3337 100644
--- a/main/src/main/scala/sbt/Defaults.scala
+++ b/main/src/main/scala/sbt/Defaults.scala
@@ -1722,10 +1722,18 @@ object Defaults extends BuildCommon {
   def packageBinMappings: Initialize[Task[Seq[(HashedVirtualFileRef, String)]]] =
     Def.task {
       val converter = fileConverter.value
+      val classDirPath = classDirectory.value.toPath.toAbsolutePath.normalize
       val xs = products.value
-      xs
+      val allMappings = xs
         .flatMap(Path.allSubpaths)
-        .withFilter(_._1.isFile())
+        .filter(_._1.isFile())
+      val resourcePaths = allMappings.collect {
+        case (p, path) if !p.toPath.toAbsolutePath.normalize.startsWith(classDirPath) => path
+      }.toSet
+      allMappings
+        .filterNot { (p, path) =>
+          resourcePaths(path) && p.toPath.toAbsolutePath.normalize.startsWith(classDirPath)
+        }
         .map { (p, path) =>
           val vf = converter.toVirtualFile(p.toPath())
           (vf: HashedVirtualFileRef) -> path
diff --git a/sbt-app/src/sbt-test/plugins/duplicate-autoplugins-packagebin/build.sbt b/sbt-app/src/sbt-test/plugins/duplicate-autoplugins-packagebin/build.sbt
new file mode 100644
index 000000000..40734b4c1
--- /dev/null
+++ b/sbt-app/src/sbt-test/plugins/duplicate-autoplugins-packagebin/build.sbt
@@ -0,0 +1,4 @@
+ThisBuild / organization := "com.example"
+ThisBuild / version      := "0.1.0-SNAPSHOT"
+
+val `scalac-options` = project.enablePlugins(SbtPlugin)
diff --git a/sbt-app/src/sbt-test/plugins/duplicate-autoplugins-packagebin/scalac-options/src/main/scala/example/ScalacOptionsPlugin.scala b/sbt-app/src/sbt-test/plugins/duplicate-autoplugins-packagebin/scalac-options/src/main/scala/example/ScalacOptionsPlugin.scala
new file mode 100644
index 000000000..3d8f9eae2
--- /dev/null
+++ b/sbt-app/src/sbt-test/plugins/duplicate-autoplugins-packagebin/scalac-options/src/main/scala/example/ScalacOptionsPlugin.scala
@@ -0,0 +1,5 @@
+package example
+
+import sbt.*
+
+object ScalacOptionsPlugin extends AutoPlugin
diff --git a/sbt-app/src/sbt-test/plugins/duplicate-autoplugins-packagebin/test b/sbt-app/src/sbt-test/plugins/duplicate-autoplugins-packagebin/test
new file mode 100644
index 000000000..e00f9cbb0
--- /dev/null
+++ b/sbt-app/src/sbt-test/plugins/duplicate-autoplugins-packagebin/test
@@ -0,0 +1,3 @@
+> scalac-options / Compile / packageBin
+> scalac-options / Compile / copyResources
+> scalac-options / Compile / packageBin