Various embodiments of methods and systems for energy efficiency aware thermal management in a portable computing device that contains a heterogeneous, multi-processor system on a chip (“SoC”) are disclosed. Because individual processing components in a heterogeneous, multi-processor SoC may exhibit different processing efficiencies at a given temperature, energy efficiency aware thermal management techniques that compare performance data of the individual processing components at their measured operating temperatures can be leveraged to optimize quality of service (“QoS”) by adjusting the power supplies to, reallocating workloads away from, or transitioning the power mode of, the least energy efficient processing components. In these ways, embodiments of the solution optimize the average amount of power consumed across the SoC to process a MIPS of workload.