A system that validates a native code module. During operation, the system receives a native code module comprised of untrusted native program code. The system validates the native code module by: (1) determining that code in the native code module does not include any restricted instructions and/or does not access restricted features of a computing device; and (2) determining that the instructions in the native code module are aligned along byte boundaries such that a specified set of byte boundaries always contain a valid instruction and control flow instructions have valid targets. The system allows successfully-validated native code modules to execute, and rejects native code modules that fail validation. By validating the native code module, the system facilitates safely executing the native code module in the secure runtime environment on the computing device, thereby achieving native code performance for untrusted program binaries without significant risk of unwanted side effects.