One embodiment of the present invention sets forth a technique for representing and managing a multi-architecture co-processor application program. Source code for co-processor functions is compiled in two stages. The first stage incorporates a majority of the computationally intensive processing steps associated with co-processor code compilation. The first stage generates virtual assembly code from the source code. The second stage generates co-processor machine code from the virtual assembly. Both the virtual assembly and co-processor machine code may be included within the co-processor enabled application program. A co-processor driver uses a description of the currently available co-processor to select between virtual assembly and co-processor machine code. If the virtual assembly code is selected, then the co-processor driver compiles the virtual assembly into machine code for the current co-processor.