diff --git a/build.sbt b/build.sbt
index 7a981fa5c..f104ee403 100644
--- a/build.sbt
+++ b/build.sbt
@@ -158,6 +158,7 @@ lazy val cli = project
     shared,
     dontPublishIn("2.10", "2.12"),
     coursierPrefix,
+    unmanagedResources.in(Test) += packageBin.in(bootstrap).in(Compile).value,
     libs ++= {
       if (scalaBinaryVersion.value == "2.11")
         Seq(
diff --git a/cli/src/main/scala-2.11/coursier/cli/Bootstrap.scala b/cli/src/main/scala-2.11/coursier/cli/Bootstrap.scala
index 5155de2ce..5ff00ac1d 100644
--- a/cli/src/main/scala-2.11/coursier/cli/Bootstrap.scala
+++ b/cli/src/main/scala-2.11/coursier/cli/Bootstrap.scala
@@ -11,7 +11,7 @@ import caseapp._
 import coursier.cli.util.Zip
 import coursier.internal.FileUtil
 
-final case class Bootstrap(
+case class Bootstrap(
   @Recurse
     artifactOptions: ArtifactOptions,
   @Recurse
@@ -96,26 +96,32 @@ final case class Bootstrap(
       options.isolated.targets.foldLeft((Vector.empty[String], Map.empty[String, (Seq[String], Seq[File])])) {
         case ((done, acc), target) =>
           val subRes = helper.res.subset(isolatedDeps.getOrElse(target, Nil).toSet)
-          val subArtifacts = subRes.artifacts.map(_.url)
 
-          val filteredSubArtifacts = subArtifacts.diff(done)
+          val (done0, subUrls, subFiles) =
+            if (options.standalone) {
+              val subFiles0 = helper.fetch(
+                sources = false,
+                javadoc = false,
+                artifactTypes = artifactOptions.artifactTypes(sources = false, javadoc = false),
+                subset = isolatedDeps.getOrElse(target, Seq.empty).toSet
+              )
 
-          def subFiles0 = helper.fetch(
-            sources = false,
-            javadoc = false,
-            artifactTypes = artifactOptions.artifactTypes(sources = false, javadoc = false),
-            subset = isolatedDeps.getOrElse(target, Seq.empty).toSet
-          )
-
-          val (subUrls, subFiles) =
-            if (options.standalone)
-              (Nil, subFiles0)
-            else
-              (filteredSubArtifacts, Nil)
+              (done, Nil, subFiles0)
+            } else {
+              val subArtifacts0 = subRes.dependencyArtifacts.map(_._2)
+              val artifactTypes = artifactOptions.artifactTypes(sources = false, javadoc = false)
+              val subArtifacts =
+                if (artifactTypes("*"))
+                  subArtifacts0
+                else
+                  subArtifacts0.filter(a => artifactTypes(a.`type`))
+              val filteredSubArtifacts = subArtifacts.map(_.url).diff(done)
+              (done ++ filteredSubArtifacts, filteredSubArtifacts, Nil)
+            }
 
           val updatedAcc = acc + (target -> (subUrls, subFiles))
 
-          (done ++ filteredSubArtifacts, updatedAcc)
+          (done0, updatedAcc)
       }
 
     val (urls, files) =
diff --git a/cli/src/test/scala-2.11/coursier/cli/CliIntegrationTest.scala b/cli/src/test/scala-2.11/coursier/cli/CliIntegrationTest.scala
index c751f1904..c8626e0a9 100644
--- a/cli/src/test/scala-2.11/coursier/cli/CliIntegrationTest.scala
+++ b/cli/src/test/scala-2.11/coursier/cli/CliIntegrationTest.scala
@@ -1,6 +1,7 @@
 package coursier.cli
 
-import java.io.{File, FileWriter}
+import java.io._
+import java.util.zip.ZipInputStream
 
 import argonaut.Argonaut._
 import coursier.cli.util.{DepNode, ReportNode}
@@ -414,4 +415,70 @@ class CliIntegrationTest extends FlatSpec {
       assert(node.dependencies.exists(_.coord.startsWith("org.scala-lang:scala-library:2.10.")))
       assert(!node.dependencies.exists(_.coord.startsWith("org.scala-lang:scala-library:2.11.")))
   }
+
+  "bootstrap" should "not add POMs to the classpath" in withFile() {
+
+    def zipEntryContent(zis: ZipInputStream, path: String): Array[Byte] = {
+      val e = zis.getNextEntry
+      if (e == null)
+        throw new NoSuchElementException(s"Entry $path in zip file")
+      else if (e.getName == path)
+        coursier.Platform.readFullySync(zis)
+      else
+        zipEntryContent(zis, path)
+    }
+
+    (bootstrapFile, _) =>
+      val artifactOptions = ArtifactOptions()
+      val common = CommonOptions(
+        repository = List("bintray:scalameta/maven")
+      )
+      val isolatedLoaderOptions = IsolatedLoaderOptions(
+        isolateTarget = List("foo"),
+        isolated = List("foo:org.scalameta:trees_2.12:1.7.0")
+      )
+      val bootstrapOptions = BootstrapOptions(
+        output = bootstrapFile.getPath,
+        isolated = isolatedLoaderOptions,
+        force = true
+      )
+
+      val bootstrap = new Bootstrap(artifactOptions, bootstrapOptions) with TestOnlyExtraArgsApp
+      bootstrap.setRemainingArgs(Seq("com.geirsson:scalafmt-cli_2.12:1.4.0"), Seq())
+      bootstrap.apply()
+
+      var fis: InputStream = null
+
+      val content = try {
+        fis = new FileInputStream(bootstrapFile)
+        coursier.Platform.readFullySync(fis)
+      } finally {
+        if (fis != null) fis.close()
+      }
+
+      val actualContent = {
+        val header = Seq[Byte](0x50, 0x4b, 0x03, 0x04)
+        val idx = content.indexOfSlice(header)
+        if (idx < 0)
+          throw new Exception(s"ZIP header not found in ${bootstrapFile.getPath}")
+        else
+          content.drop(idx)
+      }
+
+      val zis = new ZipInputStream(new ByteArrayInputStream(actualContent))
+
+      val lines = new String(zipEntryContent(zis, "bootstrap-isolation-foo-jar-urls"), "UTF-8").lines.toVector
+
+      val extensions = lines
+        .map { l =>
+          val idx = l.lastIndexOf('.')
+          if (idx < 0)
+            l
+          else
+            l.drop(idx + 1)
+        }
+        .toSet
+
+      assert(extensions == Set("jar"))
+  }
 }