Varying partial bypassing in pipelined processors is an effective way to make performance, area and energy trade-offs in embedded processors. However, performance evaluation of partial bypassing in processors has been inaccurate, largely due to the absence of bypass-sensitive retargetable compilation techniques. Furthermore no existing partial bypass exploration framework estimates the power and cost overhead of partial bypassing. In this paper we present PBExplore: A framework for Compiler-in-the-Loop exploration of partial bypassing in processors. PBExplore accurately evaluates the performance of a partially bypassed processor using a generic bypass-sensitive compilation technique. It synthesizes the bypass control logic and estimates the area and energy overhead of each bypass configuration. PBExplore is thus able to effectively perform multi-dimensional exploration of the partial bypass design space. We present experimental results on the Intel XScale architecture on MiBench benchmarks and demonstrate the need, utility and exploration capabilities of PBExplore.