Some embodiments provide a system that executes a native code module. During operation, the system obtains the native code module. Next, the system loads the native code module into a secure runtime environment. Finally, the system safely executes the native code module in the secure runtime environment by using a set of software fault isolation (SFI) mechanisms that constrain store instructions in the native code module. The SFI mechanisms also maintain control flow integrity for the native code module by dividing a code region associated with the native code module into equally sized code blocks and data blocks and starting each of the data blocks with an illegal instruction.