diff --git a/tools/cooja/build.xml b/tools/cooja/build.xml
index 05145545d..a9251360e 100644
--- a/tools/cooja/build.xml
+++ b/tools/cooja/build.xml
@@ -55,6 +55,8 @@ The COOJA Simulator
   <target name="clean" depends="init">
     <delete dir="${build}"/>
     <delete dir="${dist}"/>
+  	<ant antfile="build.xml" dir="apps/mrm" target="clean" inheritAll="false"/>
+  	<ant antfile="build.xml" dir="apps/mspsim" target="clean" inheritAll="false"/>
   </target>
 
   <target name="run" depends="init, compile, jar, copy configs">