The present invention is generally directed to various methods and systems for dynamically controlling metrology work in progress. In one illustrative embodiment, the method comprises providing a metrology control unit that is adapted to control metrology work flow to at least one metrology tool, identifying a plurality of wafer lots that are in a metrology queue wherein the wafer lots are intended to be processed in at least one metrology tool, and wherein the metrology control unit selects at least one of the wafer lots for metrology processing in the at least one metrology tool and selects at least one other of the plurality of wafer lots to be removed from the metrology queue based upon the metrology processing of the selected at least one wafer lot in the at least one metrology tool.