The generated .classpath file always sets the JRE to the default JRE in Eclipse as follows: <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/> There needs to be a way to override this so one can specify an alternate like so: <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/sun-jdk-1.4.2.08"/> In this case, the eclipse project would use the jdk that the user named "sun-jdk-1.4.2.08". An easy way to fix this is to remove the hard-coded setting in plugin.jelly and, instead, make "org.eclipse.jdt.launching.JRE_CONTAINER" the default value of the "maven.eclipse.conclasspath" property. Then in plugin.jelly, the <classpathentry kind="con" path="..."/> would always be generated with a path equal to org.eclipse.jdt.launching.JRE_CONTAINER unless the property was overriden. Carlos Sanchez helped me produce the patch. An alternate fix would be to make a new property called something like "maven.eclipse.jre" which would have a value like "sun-jdk-1.4.2.08" in which case plugin.jelly would generate: <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/sun-jdk-1.4.2.08"/> instead of <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/> Attached are patches.