A virtual machine system residing on a native machine comprises application code in a virtual machine specific format, native methods in a native machine specific format, and a plurality of execution entities that execute the application code and the native methods in parallel. An execution entity manager assigns a native method to an execution entity for execution. Based on an evaluation of the potential behavior of the native method, the execution entity manager assigns the native method to an execution entity optimized for the needs of the native method and the virtual machine system. This allows native methods that execute correctly in parallel to be assigned to an execution entity optimized to minimize system resources. Native methods that interfere with the parallel execution of other execution entities are assigned to an execution entity optimized to ensure correct native method operation.