Abstract: An apparatus and method for increasing throughput in a processor having a multi-threaded pipeline is provided. Throughput is increased by dynamically allocating hardware contexts to pipeline flows according to context issue rules. The context issue rules eliminate some hardware bypass paths allowing for a shorter clock period and minimize pipeline stalls. One context issue rule eliminates the need for an E-E bypass path by ensuring that no context is allowed to issue in two adjacent pipeline flows. Another context issue rule eliminates the need for an M-E bypass path by ensuring that data retrieved from memory in a pipeline flow for a context is available prior to a successive pipeline flow for the same context entering the execution stage. A beat issue rule looks for reduced utilization of the pipeline when no active context can issue an instruction due to the context issue rules.