The present disclosure provides a tuning system for tuning the operation of a gas turbine. The system comprises operational turbine controls for controlling operational control elements of the turbine, including at least one of turbine fuel distribution or the fuel temperature. The system also has a tuning controller communicating with the turbine controls. The tuning controller is configured to tune the operation of the turbine in accordance with the following steps: receiving operational data about the turbine, providing a hierarchy of tuning issues, determining whether sensed operational data is within predetermined operational limits and producing one or more indicators. If the operational data is not within predetermined operational limits, the tuning controller will rank the one or more indicators to determine dominant tuning concern, and tune the operation of the turbine based on dominant tuning concern. Also provided herein are a method and computer readable medium for tuning.