Options can be set with the compiler to enable certain sets of instructions. If you don't enable any Intel-specific instructions, then the application should work fine. If you did enable any Intel-specific instructions, then you can expect your application to crash if or when those instructions are called. Most compilers work the same way.
Using gcc, you can enable architecture-specific optimizations for AMD, or you can enable them for Intel, or you can compile with options set to allow portability between the two.