diff --git a/jsdependencies-sbt-plugin/src/main/scala/org/scalajs/jsdependencies/sbtplugin/JSDependenciesPlugin.scala b/jsdependencies-sbt-plugin/src/main/scala/org/scalajs/jsdependencies/sbtplugin/JSDependenciesPlugin.scala
index 833f58ba..f309c928 100644
--- a/jsdependencies-sbt-plugin/src/main/scala/org/scalajs/jsdependencies/sbtplugin/JSDependenciesPlugin.scala
+++ b/jsdependencies-sbt-plugin/src/main/scala/org/scalajs/jsdependencies/sbtplugin/JSDependenciesPlugin.scala
@@ -81,8 +81,6 @@ object JSDependenciesPlugin extends AutoPlugin {
 
   }
 
-  private lazy val memFS = Jimfs.newFileSystem()
-
   import autoImport._
 
   /** Collect certain file types from a classpath.
@@ -131,6 +129,7 @@ object JSDependenciesPlugin extends AutoPlugin {
     import java.util.zip._
 
     val jarPath = jar.getPath
+    val memFS = Jimfs.newFileSystem()
 
     val stream =
       new ZipInputStream(new BufferedInputStream(new FileInputStream(jar)))
@@ -217,7 +216,7 @@ object JSDependenciesPlugin extends AutoPlugin {
 
   private val tmpSuffixRE = """[a-zA-Z0-9-_.]*$""".r
 
-  private def tmpFile(path: String, in: InputStream): URI = {
+  private def tmpFile(path: String, in: InputStream): File = {
     try {
       /* - createTempFile requires a prefix of at least 3 chars
        * - we use a safe part of the path as suffix so the extension stays (some
@@ -228,15 +227,15 @@ object JSDependenciesPlugin extends AutoPlugin {
       val f = File.createTempFile("tmp-", suffix)
       f.deleteOnExit()
       Files.copy(in, f.toPath(), StandardCopyOption.REPLACE_EXISTING)
-      f.toURI()
+      f
     } finally {
       in.close()
     }
   }
 
-  private def materialize(file: Path): URI = {
+  private def materialize(file: Path): File = {
     try {
-      file.toFile().toURI()
+      file.toFile()
     } catch {
       case _: UnsupportedOperationException =>
         tmpFile(file.toString(), new BufferedInputStream(Files.newInputStream(file)))
@@ -401,12 +400,25 @@ object JSDependenciesPlugin extends AutoPlugin {
            */
           val libs = env match {
             case _: org.scalajs.jsenv.nodejs.NodeJSEnv =>
+              val memFS = Jimfs.newFileSystem()
+              val usedNames = mutable.Set.empty[String]
+
+              def getFileNameFor(commonJSName: String): String = {
+                var name = commonJSName
+                var suffix = 0
+                while (!usedNames.add(name)) {
+                  suffix += 1
+                  name = s"${commonJSName}_$suffix"
+                }
+                s"require-$name.js"
+              }
+
               for (dep <- deps) yield {
                 dep.info.commonJSName.fold {
                   dep.lib
                 } { commonJSName =>
-                  val fname = materialize(dep.lib).toASCIIString
-                  Files.write(memFS.getPath(s"require-$fname"),
+                  val fname = materialize(dep.lib).getAbsolutePath
+                  Files.write(memFS.getPath(getFileNameFor(commonJSName)),
                       s"""$commonJSName = require("${escapeJS(fname)}");""".getBytes(StandardCharsets.UTF_8))
                 }
               }
diff --git a/sbt-plugin-test/build.sbt b/sbt-plugin-test/build.sbt
index 2e03de19..62ff5eee 100644
--- a/sbt-plugin-test/build.sbt
+++ b/sbt-plugin-test/build.sbt
@@ -11,7 +11,8 @@ addCommandAlias("testAll",
     ";jsDependenciesTest/packageJSDependencies" +
     ";jsDependenciesTest/packageMinifiedJSDependencies" +
     ";jsDependenciesTest/regressionTestForIssue2243" +
-    ";jsNoDependenciesTest/regressionTestForIssue2243")
+    ";jsNoDependenciesTest/regressionTestForIssue2243" +
+    ";jsDependenciesRunTest/run")
 
 val regressionTestForIssue2243 = TaskKey[Unit]("regressionTestForIssue2243",
   "", KeyRanks.BTask)
@@ -114,3 +115,14 @@ lazy val jsNoDependenciesTest = withRegretionTestForIssue2243(
   project.
   enablePlugins(ScalaJSPlugin, JSDependenciesPlugin)
 )
+
+lazy val jsDependenciesRunTest =
+  project.
+  enablePlugins(ScalaJSPlugin, JSDependenciesPlugin).
+  settings(
+    scalaJSUseMainModuleInitializer := true,
+    jsDependencies ++= Seq(
+        // #40 Make sure we can run in the presence of a commonJSName
+        "org.webjars" % "mustachejs" % "0.8.2" / "mustache.js" commonJSName "Mustache",
+    ),
+  )
diff --git a/sbt-plugin-test/jsDependenciesRunTest/src/main/scala/test/Test.scala b/sbt-plugin-test/jsDependenciesRunTest/src/main/scala/test/Test.scala
new file mode 100644
index 00000000..a91dbaff
--- /dev/null
+++ b/sbt-plugin-test/jsDependenciesRunTest/src/main/scala/test/Test.scala
@@ -0,0 +1,11 @@
+package test
+
+import scala.scalajs.js
+
+object Test {
+  def main(args: Array[String]): Unit = {
+    println("Hello world")
+    assert(js.typeOf(js.Dynamic.global.Mustache) == "object")
+    assert((js.Dynamic.global.Mustache.version: Any) == "0.8.1")
+  }
+}