diff --git a/community-build/src/scala/dotty/communitybuild/projects.scala b/community-build/src/scala/dotty/communitybuild/projects.scala
index 3856ce4e8b22..37c8b5df1adb 100644
--- a/community-build/src/scala/dotty/communitybuild/projects.scala
+++ b/community-build/src/scala/dotty/communitybuild/projects.scala
@@ -15,6 +15,9 @@ lazy val sbtPluginFilePath: String =
   new File(sys.props("user.home") + "/.sbt/1.0/plugins").mkdirs()
   communitybuildDir.resolve("sbt-dotty-sbt").toAbsolutePath().toString()
 
+lazy val sbtScalaJSPluginFilePath: String =
+  communitybuildDir.resolve("sbt-scalajs-sbt").toAbsolutePath().toString()
+
 def log(msg: String) = println(Console.GREEN + msg + Console.RESET)
 
 /** Executes shell command, returns false in case of error. */
@@ -65,6 +68,7 @@ final case class SbtCommunityProject(
     project: String,
     sbtTestCommand: String,
     extraSbtArgs: List[String] = Nil,
+    forceUpgradeSbtScalajsPlugin: Boolean = false,
     dependencies: List[CommunityProject] = Nil,
     sbtPublishCommand: String = null) extends CommunityProject:
   override val binaryName: String = "sbt"
@@ -77,10 +81,14 @@ final case class SbtCommunityProject(
     val sbtProps = Option(System.getProperty("sbt.ivy.home")) match
       case Some(ivyHome) => List(s"-Dsbt.ivy.home=$ivyHome")
       case _ => Nil
+    val scalaJSPluginArgs =
+      if (forceUpgradeSbtScalajsPlugin) List(s"--addPluginSbtFile=$sbtScalaJSPluginFilePath")
+      else Nil
     extraSbtArgs ++ sbtProps ++ List(
       "-sbt-version", "1.3.8",
        "-Dsbt.supershell=false",
-      s"--addPluginSbtFile=$sbtPluginFilePath")
+      s"--addPluginSbtFile=$sbtPluginFilePath"
+    ) ++ scalaJSPluginArgs
 
 object projects:
   lazy val utest = MillCommunityProject(
@@ -310,7 +318,8 @@ object projects:
 
   lazy val catsEffect2 = SbtCommunityProject(
     project        = "cats-effect-2",
-    sbtTestCommand = "test"
+    sbtTestCommand = "test",
+    forceUpgradeSbtScalajsPlugin = true
   )
 
   lazy val catsEffect3 = SbtCommunityProject(
diff --git a/project/Build.scala b/project/Build.scala
index 97f111b77f78..7b761dc32694 100644
--- a/project/Build.scala
+++ b/project/Build.scala
@@ -935,6 +935,7 @@ object Build {
 
       fetchScalaJSSource := {
         import org.eclipse.jgit.api._
+        import org.eclipse.jgit.lib._
 
         val s = streams.value
         val ver = scalaJSVersion
@@ -946,12 +947,14 @@ object Build {
           new CloneCommand()
             .setDirectory(trgDir)
             .setURI("https://github.com/scala-js/scala-js.git")
+            .setNoCheckout(true)
             .call()
         }
 
         // Checkout proper ref. We do this anyway so we fail if something is wrong
         val git = Git.open(trgDir)
         s.log.info(s"Checking out Scala.js source version $ver")
+        git.getRepository().getConfig().setEnum("core", null, "autocrlf", CoreConfig.AutoCRLF.FALSE)
         git.checkout().setName(s"v$ver").call()
 
         trgDir
@@ -1029,7 +1032,7 @@ object Build {
           ++ (dir / "shared/src/test/require-jdk7" ** "*.scala").get
 
           ++ (dir / "js/src/test/scala" ** (("*.scala": FileFilter)
-            -- "ExportsTest.scala" // JS exports + do not compile because of a var in a structural type
+            -- "ExportsTest.scala" // JS exports + IR checking error
             -- "ObjectTest.scala" // compile errors caused by #9588
             -- "StackTraceTest.scala" // would require `npm install source-map-support`
             -- "UnionTypeTest.scala" // requires the Scala 2 macro defined in Typechecking*.scala
@@ -1045,12 +1048,8 @@ object Build {
       // Putting them here instead of above makes sure that we do not regress on compilation+linking.
       Test / testOptions += Tests.Filter { name =>
         !Set[String](
-          "org.scalajs.testsuite.compiler.InteroperabilityTest", // 3 tests require JS exports, all other tests pass
-
           "org.scalajs.testsuite.jsinterop.AsyncTest", // needs JS exports in PromiseMock.scala
-          "org.scalajs.testsuite.jsinterop.DynamicTest", // one test requires JS exports, all other tests pass
           "org.scalajs.testsuite.jsinterop.JSExportStaticTest", // JS exports
-          "org.scalajs.testsuite.jsinterop.NonNativeJSTypeTest", // 1 test fails because of a progression for value class fields (needs an update upstream)
 
           // Not investigated so far
           "org.scalajs.testsuite.junit.JUnitAbstractClassTestCheck",
@@ -1205,6 +1204,9 @@ object Build {
           s"""updateOptions in Global ~= (_.withLatestSnapshots(false))
              |addSbtPlugin("ch.epfl.lamp" % "sbt-dotty" % "$sbtDottyVersion")""".stripMargin
         IO.write(baseDirectory.value / "sbt-dotty-sbt", pluginText)
+        val scalaJSPluginText =
+          s"""addSbtPlugin("org.scala-js" % "sbt-scalajs" % "$scalaJSVersion")\n"""
+        IO.write(baseDirectory.value / "sbt-scalajs-sbt", scalaJSPluginText)
         IO.write(baseDirectory.value / "scala3-bootstrapped.version", dottyVersion)
       },
       testOptions in Test += Tests.Argument(
diff --git a/project/plugins.sbt b/project/plugins.sbt
index 924c174b3c7c..6f83bef934f9 100644
--- a/project/plugins.sbt
+++ b/project/plugins.sbt
@@ -2,7 +2,7 @@
 //
 // e.g. addSbtPlugin("com.github.mpeltonen" % "sbt-idea" % "1.1.0")
 
-addSbtPlugin("org.scala-js" % "sbt-scalajs" % "1.2.0")
+addSbtPlugin("org.scala-js" % "sbt-scalajs" % "1.3.0")
 
 addSbtPlugin("org.xerial.sbt" % "sbt-sonatype" % "3.6")
 
diff --git a/sbt-dotty/sbt-test/scalajs/basic/project/plugins.sbt b/sbt-dotty/sbt-test/scalajs/basic/project/plugins.sbt
index 0cd6969bf6e2..70503e9f7c7a 100644
--- a/sbt-dotty/sbt-test/scalajs/basic/project/plugins.sbt
+++ b/sbt-dotty/sbt-test/scalajs/basic/project/plugins.sbt
@@ -1,2 +1,2 @@
 addSbtPlugin("ch.epfl.lamp" % "sbt-dotty" % sys.props("plugin.version"))
-addSbtPlugin("org.scala-js" % "sbt-scalajs" % "1.2.0")
+addSbtPlugin("org.scala-js" % "sbt-scalajs" % "1.3.0")