diff --git a/main/define/src/mill/define/Discover.scala b/main/define/src/mill/define/Discover.scala
index c3136c2a0a0..03316412f80 100644
--- a/main/define/src/mill/define/Discover.scala
+++ b/main/define/src/mill/define/Discover.scala
@@ -141,11 +141,20 @@ object Discover {
         }
         if overridesRoutes._1.nonEmpty || overridesRoutes._2.nonEmpty || overridesRoutes._3.nonEmpty
       } yield {
+        val lhs0 = discoveredModuleType match {
+          // Explicitly do not de-alias type refs, so type aliases to deprecated
+          // types do not result in spurious deprecation warnings appearing
+          case tr: TypeRef => tr
+          // Other types are fine
+          case _ => discoveredModuleType.typeSymbol.asClass.toType
+        }
+
+        val lhs = q"classOf[$lhs0]"
+
         // by wrapping the `overridesRoutes` in a lambda function we kind of work around
         // the problem of generating a *huge* macro method body that finally exceeds the
         // JVM's maximum allowed method size
         val overridesLambda = q"(() => $overridesRoutes)()"
-        val lhs = q"classOf[${discoveredModuleType.typeSymbol.asClass}]"
         q"$lhs -> $overridesLambda"
       }
 
diff --git a/runner/src/mill/runner/CodeGen.scala b/runner/src/mill/runner/CodeGen.scala
index fa75337cb4c..58d549d69a5 100644
--- a/runner/src/mill/runner/CodeGen.scala
+++ b/runner/src/mill/runner/CodeGen.scala
@@ -161,11 +161,7 @@ object CodeGen {
         newScriptCode = objectData.name.applyTo(newScriptCode, wrapperObjectName)
         newScriptCode = objectData.obj.applyTo(newScriptCode, "abstract class")
 
-        val millDiscover =
-          if (segments.nonEmpty) ""
-          else
-            """@_root_.scala.annotation.nowarn
-              |  override lazy val millDiscover: _root_.mill.define.Discover = _root_.mill.define.Discover[this.type]""".stripMargin
+        val millDiscover = discoverSnippet(segments)
 
         s"""$pkgLine
            |$aliasImports
@@ -224,11 +220,7 @@ object CodeGen {
       s"extends _root_.mill.main.RootModule.Subfolder "
     }
 
-    val millDiscover =
-      if (segments.nonEmpty) ""
-      else
-        """@_root_.scala.annotation.nowarn
-          |  override lazy val millDiscover: _root_.mill.define.Discover = _root_.mill.define.Discover[this.type]""".stripMargin
+    val millDiscover = discoverSnippet(segments)
 
     // User code needs to be put in a separate class for proper submodule
     // object initialization due to https://github.com/scala/scala3/issues/21444
@@ -240,6 +232,14 @@ object CodeGen {
 
   }
 
+  def discoverSnippet(segments: Seq[String]): String = {
+    if (segments.nonEmpty) ""
+    else
+      """override lazy val millDiscover: _root_.mill.define.Discover = _root_.mill.define.Discover[this.type]
+        |""".stripMargin
+
+  }
+
   private case class Snippet(var text: String = null, var start: Int = -1, var end: Int = -1) {
     def applyTo(s: String, replacement: String): String =
       s.patch(start, replacement.padTo(end - start, ' '), end - start)