Many modern measurement methods for heat transfer work in the frequency domain. A certain average temperature rise in the sample is unavoidable if the sample can only be heated, e.g., by an intensity modulated light source. This average temperature rise influences the measured thermal properties because they are, in general, temperature dependent. Here, we explore square waves and multiplexed sine waves with the goal of reducing the average temperature rise. We apply these signals to lock-in thermography and show the feasibility of a simultaneous measurement at multiple frequencies. In addition, we propose the use of the Goertzel algorithm to efficiently extract individual spectral components from the temperature signal.