diff --git a/project/Build.scala b/project/Build.scala
index 2e6e7a242389..a618c5f21768 100644
--- a/project/Build.scala
+++ b/project/Build.scala
@@ -36,15 +36,6 @@ object MyScalaJSPlugin extends AutoPlugin {
   override def projectSettings: Seq[Setting[_]] = Def.settings(
     commonBootstrappedSettings,
 
-    /* Remove the Scala.js compiler plugin for scalac, and enable the
-     * Scala.js back-end of dotty instead.
-     */
-    libraryDependencies := {
-      val deps = libraryDependencies.value
-      deps.filterNot(_.name.startsWith("scalajs-compiler")).map(_.withDottyCompat(scalaVersion.value))
-    },
-    scalacOptions += "-scalajs",
-
     // Replace the JVM JUnit dependency by the Scala.js one
     libraryDependencies ~= {
       _.filter(!_.name.startsWith("junit-interface"))
@@ -289,8 +280,11 @@ object Build {
       Some((packageBin in (`dotty-sbt-bridge`, Compile)).value)
     },
 
-    // Use the same name as the non-bootstrapped projects for the artifacts
-    moduleName ~= { _.stripSuffix("-bootstrapped") },
+    // Use the same name as the non-bootstrapped projects for the artifacts.
+    // Remove the `js` suffix because JS artifacts are published using their special crossVersion.
+    // The order of the two `stripSuffix`es is important, so that
+    // dotty-library-bootstrappedjs becomes dotty-library.
+    moduleName ~= { _.stripSuffix("js").stripSuffix("-bootstrapped") },
 
     // Enforce that the only Scala 2 classfiles we unpickle come from scala-library
     /*
@@ -778,8 +772,14 @@ object Build {
     asDottyLibrary(Bootstrapped).
     enablePlugins(MyScalaJSPlugin).
     settings(
+      libraryDependencies +=
+        ("org.scala-js" %% "scalajs-library" % scalaJSVersion).withDottyCompat(scalaVersion.value),
       unmanagedSourceDirectories in Compile :=
         (unmanagedSourceDirectories in (`dotty-library-bootstrapped`, Compile)).value,
+
+      // Make sure `dotty-bootstrapped/test` doesn't fail on this project for no reason
+      test in Test := {},
+      testOnly in Test := {},
     )
 
   lazy val tastyCoreSettings = Seq(
@@ -1397,7 +1397,8 @@ object Build {
     def asDottyRoot(implicit mode: Mode): Project = project.withCommonSettings.
       aggregate(`dotty-interfaces`, dottyLibrary, dottyCompiler, tastyCore, dottyDoc, `dotty-sbt-bridge`).
       bootstrappedAggregate(`scala-library`, `scala-compiler`, `scala-reflect`, scalap,
-        `dotty-language-server`, `dotty-staging`, `dotty-tasty-inspector`, `dotty-tastydoc`).
+        `dotty-language-server`, `dotty-staging`, `dotty-tasty-inspector`, `dotty-tastydoc`,
+        `dotty-library-bootstrappedJS`).
       dependsOn(tastyCore).
       dependsOn(dottyCompiler).
       dependsOn(dottyLibrary).
diff --git a/sbt-dotty/sbt-test/scalajs/basic/Main.scala b/sbt-dotty/sbt-test/scalajs/basic/Main.scala
new file mode 100644
index 000000000000..fdee6e6bef11
--- /dev/null
+++ b/sbt-dotty/sbt-test/scalajs/basic/Main.scala
@@ -0,0 +1,11 @@
+package test
+
+import scala.scalajs.js
+import org.scalajs.dom
+
+object Main {
+  def main(args: Array[String]): Unit = {
+    println("Hello Scala.js")
+    dom.console.log("using a Scala.js dependency")
+  }
+}
diff --git a/sbt-dotty/sbt-test/scalajs/basic/build.sbt b/sbt-dotty/sbt-test/scalajs/basic/build.sbt
new file mode 100644
index 000000000000..53f8bc4e52e6
--- /dev/null
+++ b/sbt-dotty/sbt-test/scalajs/basic/build.sbt
@@ -0,0 +1,8 @@
+enablePlugins(ScalaJSPlugin)
+
+scalaVersion := sys.props("plugin.scalaVersion")
+
+// Test withDottyCompat for %%% dependencies
+libraryDependencies += ("org.scala-js" %%% "scalajs-dom" % "1.1.0").withDottyCompat(scalaVersion.value)
+
+scalaJSUseMainModuleInitializer := true
diff --git a/sbt-dotty/sbt-test/scalajs/basic/project/plugins.sbt b/sbt-dotty/sbt-test/scalajs/basic/project/plugins.sbt
new file mode 100644
index 000000000000..1c988055f92e
--- /dev/null
+++ b/sbt-dotty/sbt-test/scalajs/basic/project/plugins.sbt
@@ -0,0 +1,2 @@
+addSbtPlugin("ch.epfl.lamp" % "sbt-dotty" % sys.props("plugin.version"))
+addSbtPlugin("org.scala-js" % "sbt-scalajs" % "1.1.1")
diff --git a/sbt-dotty/sbt-test/scalajs/basic/test b/sbt-dotty/sbt-test/scalajs/basic/test
new file mode 100644
index 000000000000..62ea636c177f
--- /dev/null
+++ b/sbt-dotty/sbt-test/scalajs/basic/test
@@ -0,0 +1 @@
+> run
diff --git a/sbt-dotty/src/dotty/tools/sbtplugin/DottyPlugin.scala b/sbt-dotty/src/dotty/tools/sbtplugin/DottyPlugin.scala
index 5b7a2bb5fd03..4c9dffdc034f 100644
--- a/sbt-dotty/src/dotty/tools/sbtplugin/DottyPlugin.scala
+++ b/sbt-dotty/src/dotty/tools/sbtplugin/DottyPlugin.scala
@@ -16,6 +16,7 @@ import scala.util.Properties.isJavaAtLeast
 object DottyPlugin extends AutoPlugin {
   object autoImport {
     val isDotty = settingKey[Boolean]("Is this project compiled with Dotty?")
+    val isDottyJS = settingKey[Boolean]("Is this project compiled with Dotty and Scala.js?")
 
     // NOTE:
     // - this is a def to support `scalaVersion := dottyLatestNightlyBuild`
@@ -93,7 +94,7 @@ object DottyPlugin extends AutoPlugin {
         val name = moduleID.name
         if (name != "dotty" && name != "dotty-library" && name != "dotty-compiler")
           moduleID.crossVersion match {
-            case _: librarymanagement.Binary =>
+            case binary: librarymanagement.Binary =>
               val compatVersion =
                 CrossVersion.partialVersion(scalaVersion) match {
                   case Some((3, _)) =>
@@ -107,7 +108,7 @@ object DottyPlugin extends AutoPlugin {
                     ""
                 }
               if (compatVersion.nonEmpty)
-                moduleID.cross(CrossVersion.constant(compatVersion))
+                moduleID.cross(CrossVersion.constant(binary.prefix + compatVersion + binary.suffix))
               else
                 moduleID
             case _ =>
@@ -170,6 +171,29 @@ object DottyPlugin extends AutoPlugin {
     Seq(
       isDotty := scalaVersion.value.startsWith("0.") || scalaVersion.value.startsWith("3."),
 
+      /* The way the integration with Scala.js works basically assumes that the settings of ScalaJSPlugin
+       * will be applied before those of DottyPlugin. It seems to be the case in the tests I did, perhaps
+       * because ScalaJSPlugin is explicitly enabled, while DottyPlugin is triggered. However, I could
+       * not find an authoritative source on the topic.
+       *
+       * There is an alternative implementation that would not have that assumption: it would be to have
+       * another DottyJSPlugin, that would be auto-triggered by the presence of *both* DottyPlugin and
+       * ScalaJSPlugin. That plugin would be guaranteed to have its settings be applied after both of them,
+       * by the documented rules. However, that would require sbt-dotty to depend on sbt-scalajs to be
+       * able to refer to ScalaJSPlugin.
+       *
+       * When the logic of sbt-dotty moves to sbt itself, the logic specific to the Dotty-Scala.js
+       * combination will have to move to sbt-scalajs. Doing so currently wouldn't work since we
+       * observe that the settings of DottyPlugin are applied after ScalaJSPlugin, so ScalaJSPlugin
+       * wouldn't be able to fix up things like the dependency on dotty-library.
+       */
+      isDottyJS := {
+        isDotty.value && (crossVersion.value match {
+          case binary: librarymanagement.Binary => binary.prefix.contains("sjs1_")
+          case _                                => false
+        })
+      },
+
       scalaOrganization := {
         if (isDotty.value)
           "ch.epfl.lamp"
@@ -317,12 +341,51 @@ object DottyPlugin extends AutoPlugin {
 
       // Because managedScalaInstance is false, sbt won't add the standard library to our dependencies for us
       libraryDependencies ++= {
-        if (isDotty.value && autoScalaLibrary.value)
-          Seq(scalaOrganization.value %% "dotty-library" % scalaVersion.value)
-        else
+        if (isDotty.value && autoScalaLibrary.value) {
+          val name =
+            if (isDottyJS.value) "dotty-library_sjs1"
+            else "dotty-library"
+          Seq(scalaOrganization.value %% name % scalaVersion.value)
+        } else
           Seq()
       },
 
+      // Patch up some more options if this is Dotty with Scala.js
+      scalacOptions := {
+        val prev = scalacOptions.value
+        /* The `&& !prev.contains("-scalajs")` is future-proof, for when sbt-scalajs adds that
+         * option itself but sbt-dotty is still required for the other Dotty-related stuff.
+         */
+        if (isDottyJS.value && !prev.contains("-scalajs")) prev :+ "-scalajs"
+        else prev
+      },
+      libraryDependencies := {
+        val prev = libraryDependencies.value
+        if (!isDottyJS.value) {
+          prev
+        } else {
+          prev
+            /* Remove the dependencies we don't want:
+             * * We don't want scalajs-library, because we need the one that comes
+             *   as a dependency of dotty-library_sjs1
+             * * We don't want scalajs-compiler, because that's a compiler plugin,
+             *   which is replaced by the `-scalajs` flag in dotc.
+             */
+            .filterNot { moduleID =>
+              moduleID.organization == "org.scala-js" && (
+                moduleID.name == "scalajs-library" || moduleID.name == "scalajs-compiler"
+              )
+            }
+            // Apply withDottyCompat to the dependency on scalajs-test-bridge
+            .map { moduleID =>
+              if (moduleID.organization == "org.scala-js" && moduleID.name == "scalajs-test-bridge")
+                moduleID.withDottyCompat(scalaVersion.value)
+              else
+                moduleID
+            }
+        }
+      },
+
       // Turns off the warning:
       // [warn] Binary version (0.9.0-RC1) for dependency ...;0.9.0-RC1
       // [warn]  in ... differs from Scala binary version in project (0.9).