diff --git a/project/Build.scala b/project/Build.scala
index 4cda2cda5135..91ca2d2960b6 100644
--- a/project/Build.scala
+++ b/project/Build.scala
@@ -1419,6 +1419,7 @@ object Build {
 
   /* Configuration of the org.scala-lang:scala-library:*.**.**-nonboostrapped project */
   lazy val `scala-library-nonbootstrapped` = project.in(file("library"))
+    .enablePlugins(ScalaLibraryPlugin)
     .settings(
       name          := "scala-library-nonbootstrapped",
       moduleName    := "scala-library",
@@ -1448,6 +1449,7 @@ object Build {
 
   /* Configuration of the org.scala-lang:scala-library:*.**.**-boostrapped project */
   lazy val `scala-library-bootstrapped` = project.in(file("library"))
+    .enablePlugins(ScalaLibraryPlugin)
     .settings(
       name          := "scala-library-bootstrapped",
       moduleName    := "scala-library",
@@ -1474,8 +1476,11 @@ object Build {
       publish / skip := true,
       // Project specific target folder. sbt doesn't like having two projects using the same target folder
       target := target.value / "scala-library-bootstrapped",
+      // we need to have the `scala-library` artifact in the classpath for `ScalaLibraryPlugin` to work
+      // this was the only way to not get the artifact evicted by sbt. Even a custom configuration didn't work
+      // NOTE: true is the default value, just making things clearer here
+      managedScalaInstance := true,
       // Configure the nonbootstrapped compiler
-      managedScalaInstance := false,
       scalaInstance := {
         val externalLibraryDeps = (`scala3-library` / Compile / externalDependencyClasspath).value.map(_.data).toSet
         val externalCompilerDeps = (`scala3-compiler` / Compile / externalDependencyClasspath).value.map(_.data).toSet
@@ -1494,7 +1499,7 @@ object Build {
         val compilerJars = Seq(tastyCore, scala3Interfaces, scala3Compiler) ++ (externalCompilerDeps -- externalLibraryDeps)
 
         Defaults.makeScalaInstance(
-          scalaVersion.value,
+          dottyNonBootstrappedVersion,
           libraryJars = libraryJars,
           allCompilerJars = compilerJars,
           allDocJars = Seq.empty,
diff --git a/project/ScalaLibraryPlugin.scala b/project/ScalaLibraryPlugin.scala
index 2eac7271644a..a0d4dda50883 100644
--- a/project/ScalaLibraryPlugin.scala
+++ b/project/ScalaLibraryPlugin.scala
@@ -4,13 +4,14 @@ import sbt.*
 import sbt.Keys.*
 import scala.jdk.CollectionConverters.*
 import java.nio.file.Files
+import xsbti.VirtualFileRef
+import sbt.internal.inc.Stamper
 
 object ScalaLibraryPlugin extends AutoPlugin {
 
   override def trigger = noTrigger
 
   val fetchScala2ClassFiles = taskKey[(Set[File], File)]("Fetch the files to use that were compiled with Scala 2")
-  //val scala2LibraryVersion  = settingKey[String]("Version of the Scala 2 Standard Library")
 
   override def projectSettings = Seq (
     fetchScala2ClassFiles := {
@@ -37,17 +38,29 @@ object ScalaLibraryPlugin extends AutoPlugin {
       } (Set(scalaLibraryBinaryJar)), target)
 
     },
-    (Compile / compile) := {
+    (Compile / manipulateBytecode) := {
       val stream = streams.value
       val target = (Compile / classDirectory).value
       val (files, reference) = fetchScala2ClassFiles.value;
-      val analysis = (Compile / compile).value
-      stream.log.info(s"Copying files from Scala 2 Standard Library to $target")
-      for (file <- files; id <- file.relativeTo(reference).map(_.toString())) {
-        if (filesToCopy(id)) {
-          stream.log.debug(s"Copying file '${id}' to ${target / id}")
-          IO.copyFile(file, target / id)
-        }
+      val previous = (Compile / manipulateBytecode).value
+      val analysis = previous.analysis match {
+        case analysis: sbt.internal.inc.Analysis => analysis
+        case _ => sys.error("Unexpected analysis type")
+      }
+
+      var stamps = analysis.stamps
+      for (file <- files; 
+           id <- file.relativeTo(reference); 
+           if filesToCopy(id.toString()); // Only Override Some Very Specific Files
+           dest = target / (id.toString); 
+           ref <- dest.relativeTo((LocalRootProject / baseDirectory).value)
+          ) { 
+        // Copy the files to the classDirectory
+        IO.copyFile(file, dest)
+        // Update the timestamp in the analysis
+        stamps = stamps.markProduct(
+          VirtualFileRef.of(s"$${BASE}/$ref"), 
+          Stamper.forFarmHashP(dest.toPath()))
       }
 
       val overwrittenBinaries = Files.walk((Compile / classDirectory).value.toPath())
@@ -56,13 +69,18 @@ object ScalaLibraryPlugin extends AutoPlugin {
         .map(_.toFile)
         .map(_.relativeTo((Compile / classDirectory).value).get)
         .toSet
+
       val diff = files.filterNot(_.relativeTo(reference).exists(overwrittenBinaries))
 
-      IO.copy(diff.map { file =>
-        file -> (Compile / classDirectory).value / file.relativeTo(reference).get.getPath
-      })
+      // Copy all the specialized classes in the stdlib
+      // no need to update any stamps as these classes exist nowhere in the analysis
+      for (orig <- diff; dest <- orig.relativeTo(reference)) {
+        IO.copyFile(orig, ((Compile / classDirectory).value / dest.toString()))
+      }
 
-      analysis
+      previous
+        .withAnalysis(analysis.copy(stamps = stamps)) // update the analysis with the correct stamps
+        .withHasModified(true)  // mark it as updated for sbt to update its caches
     }
   )