A method, system and computer program product are provided for implementing coherent accelerator function isolation for virtualization in an input/output (IO) adapter in a computer system. A coherent accelerator provides accelerator function units (AFUs), each AFU is adapted to operate independently of the other AFUs to perform a computing task that can be implemented within application software on a processor. The AFU has access to system memory bound to the application software and is adapted to make copies of that memory within AFU memory-cache in the AFU. As part of this memory coherency domain, each of the AFU memory-cache and processor memory-cache is adapted to be aware of changes to data commonly in either cache as well as data changed in memory of which the respective cache contains a copy.