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..8a2af54e 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)))
@@ -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"),
+                  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..517dd56c 100644
--- a/sbt-plugin-test/build.sbt
+++ b/sbt-plugin-test/build.sbt
@@ -10,6 +10,7 @@ name := "sbt-plugin-test"
 addCommandAlias("testAll",
     ";jsDependenciesTest/packageJSDependencies" +
     ";jsDependenciesTest/packageMinifiedJSDependencies" +
+    ";jsDependenciesTest/jsEnvInput" + // #40
     ";jsDependenciesTest/regressionTestForIssue2243" +
     ";jsNoDependenciesTest/regressionTestForIssue2243")