Systems and methods for synchronizing multiple processing engines of a microprocessor. In a microprocessor engine employing processor extension logic, DMA engines are used to permit the processor extension logic to move data into and out of local memory independent of the main instruction pipeline. Synchronization between the extended instruction pipeline and DMA engines is performed to maximize simultaneous operation of these elements. The DMA engines includes a data-in and data-out engine each adapted to buffer at least one instruction in a queue. If, for each DMA engine, the queue is full and a new instruction is trying to enter the buffer, the DMA engine will cause the extended pipeline to pause execution until the current DMA operation is complete. This prevents data overwrites while maximizing simultaneous operation.