diff --git a/cli/src/main/scala-2.12/coursier/cli/Bootstrap.scala b/cli/src/main/scala-2.12/coursier/cli/Bootstrap.scala
index 5f971d2ec..e9d1b6544 100644
--- a/cli/src/main/scala-2.12/coursier/cli/Bootstrap.scala
+++ b/cli/src/main/scala-2.12/coursier/cli/Bootstrap.scala
@@ -68,18 +68,37 @@ object Bootstrap extends CaseApp[BootstrapOptions] {
 
   private def createJarBootstrapWithPreamble(javaOpts: Seq[String], output: File, content: Array[Byte]): Unit = {
 
+    val argsPartitioner =
+      """|sys_args=""
+         |app_args=""
+         |i=1; while [ "$i" -le $# ]; do
+         |  eval arg=\${$i}
+         |  case $arg in
+         |    -J-*)
+         |      sys_args="$sys_args ${arg#-J}"
+         |      ;;
+         |    *)
+         |      app_args="$app_args $arg"
+         |      ;;
+         |  esac
+         |  i=$((i + 1))
+         |done
+         |""".stripMargin
+
     val javaCmd = Seq("java") ++
       javaOpts
         // escaping possibly a bit loose :-|
         .map(s => "'" + s.replace("'", "\\'") + "'") ++
       Seq(
+        "$sys_args",
         "-jar",
         "\"$0\"",
-        "\"$@\""
+        "$app_args"
       )
 
     val shellPreamble = Seq(
       "#!/usr/bin/env sh",
+      argsPartitioner,
       "exec " + javaCmd.mkString(" ")
     ).mkString("", "\n", "\n")
 
diff --git a/scripts/travis.sh b/scripts/travis.sh
index 2a8ee09ce..e16006a8f 100755
--- a/scripts/travis.sh
+++ b/scripts/travis.sh
@@ -136,6 +136,11 @@ testBootstrap() {
       exit 1
     fi
 
+    if [ "$(./cs-echo-launcher -J-Dother=thing foo -J-Dfoo=baz)" != foo ]; then
+      echo "Error: unexpected output from bootstrapped echo command (generated by proguarded launcher)." 1>&2
+      exit 1
+    fi
+
     # run via the launcher rather than via the sbt-pack scripts, because the latter interprets -Dfoo=baz itself
     # rather than passing it to coursier since https://github.com/xerial/sbt-pack/pull/118
     ./coursier-test bootstrap -o cs-props -D other=thing -J -Dfoo=baz io.get-coursier:props:1.0.2
@@ -150,6 +155,11 @@ testBootstrap() {
       exit 1
     fi
 
+    if [ "$(./cs-props -J-Dhappy=days happy)" != days ]; then
+      echo "Error: unexpected output from bootstrapped props command." 1>&2
+      exit 1
+    fi
+
     # assembly tests
     ./coursier-test bootstrap -a -o cs-props-assembly -D other=thing -J -Dfoo=baz io.get-coursier:props:1.0.2
     local OUT="$(./cs-props-assembly foo)"
@@ -192,6 +202,8 @@ if isScalaJs; then
   jsCompile
   runJsTests
 else
+  testBootstrap
+
   testNativeBootstrap
 
   integrationTestsRequirements
@@ -208,8 +220,6 @@ else
   else
     runJvmTests
 
-    testBootstrap
-
     validateReadme
     checkBinaryCompatibility
   fi