An auto-tune controller and tuning process implemented thereby for measuring and tuning the combustion dynamics and emissions of a GT engine, relative to predetermined upper limits, are provided. Initially, the tuning process includes monitoring the combustion dynamics of a plurality of combustors and emissions for a plurality of conditions. Upon determination that one or more of the conditions exceeds a predetermined upper limit, a fuel flow split to a fuel circuit on all of the combustors on the engine is adjusted by a predetermined amount. The control system continues to monitor the combustion dynamics and to recursively adjust the fuel flow split by the predetermined amount until the combustion dynamics and/or emissions are operating within a prescribed range of the GT engine. Additionally, a method of automated extended turndown of a GT engine to find a minimum load is provided.