One embodiment provides a system that protects translated guest program code in a virtual machine that supports self-modifying program code. While executing a guest program in the virtual machine, the system uses a guest shadow page table associated with the guest program and the virtual machine to map a virtual memory page for the guest program to a physical memory page on the host computing device. The system then uses a dynamic compiler to translate guest program code in the virtual memory page into translated guest program code (e.g., native program instructions for the computing device). During compilation, the dynamic compiler stores in a compiler shadow page table and the guest shadow page table information that tracks whether the guest program code in the virtual memory page has been translated. The compiler subsequently uses the information stored in the guest shadow page table to detect attempts to modify the contents of the virtual memory page. Upon detecting such an attempt, the system invalidates the translated guest program code associated with the virtual memory page.