diff --git a/modules/cli/src/main/scala/scala/cli/commands/doc/Doc.scala b/modules/cli/src/main/scala/scala/cli/commands/doc/Doc.scala
index aa7cc96898..e6a6b61435 100644
--- a/modules/cli/src/main/scala/scala/cli/commands/doc/Doc.scala
+++ b/modules/cli/src/main/scala/scala/cli/commands/doc/Doc.scala
@@ -273,8 +273,19 @@ object Doc extends ScalaCommand[DocOptions] with BuildCommandHelpers {
               .getOrElse(true)
           then defaultScaladocArgs(scalaParams.scalaVersion, javaVersion)
           else Nil
+        // scaladoc has its own `-scalajs` flag, but passing it on triggers JS backend
+        // codegen phases (e.g. JUnitBootstrappers) that crash on otherwise valid code
+        // (VirtusLab/scala-cli#3006). The doc content is platform-agnostic, so drop it.
+        val (scalaJsScalacOptions, otherScalacOptions) = builds.head.project.scalaCompiler
+          .map(_.scalacOptions).getOrElse(Nil)
+          .partition(_ == "-scalajs")
+        if scalaJsScalacOptions.nonEmpty then
+          logger.log(
+            s"Not passing ${scalaJsScalacOptions.mkString(", ")} to scaladoc, " +
+              "as it can cause it to crash on valid code (VirtusLab/scala-cli#3006)"
+          )
         val args = baseArgs ++
-          builds.head.project.scalaCompiler.map(_.scalacOptions).getOrElse(Nil) ++
+          otherScalacOptions ++
           extraArgs ++
           defaultArgs ++
           builds.map(_.output.toString)
diff --git a/modules/integration/src/test/scala/scala/cli/integration/DocTestDefinitions.scala b/modules/integration/src/test/scala/scala/cli/integration/DocTestDefinitions.scala
index ccfaa3f3e0..f80612d740 100644
--- a/modules/integration/src/test/scala/scala/cli/integration/DocTestDefinitions.scala
+++ b/modules/integration/src/test/scala/scala/cli/integration/DocTestDefinitions.scala
@@ -190,4 +190,26 @@ abstract class DocTestDefinitions
       }
     }
   }
+
+  // `-scalajs` triggers JS codegen phases (e.g. JUnitBootstrappers) that crash on valid code
+  if (!actualScalaVersion.startsWith("2."))
+    test("generate scala doc for a Scala.js project") {
+      val dest = os.rel / "doc-js"
+      TestInputs(
+        os.rel / "Hello.scala" ->
+          """/** Greeter. */
+            |object Hello {
+            |  def greet: String = "hi"
+            |}
+            |""".stripMargin
+      ).fromRoot { root =>
+        os.proc(TestUtil.cli, "doc", extraOptions, "--js", ".", "-o", dest).call(
+          cwd = root,
+          stdin = os.Inherit,
+          stdout = os.Inherit
+        )
+        expect(os.isDir(root / dest))
+        expect(os.list(root / dest).exists(_.last.endsWith(".html")))
+      }
+    }
 }