In this paper, a novel non‐linear model‐based approach is presented for maximum power point (MPP) tracking of thermoelectric generators (TEGs) using the backstepping controller. Considering the output voltage range of the thermoelectric devices, a step‐up DC–DC converter is employed as an interface between the load and input power source. According to the maximum power transfer theorem, if the equivalent input resistance of the converter (Rin) is equal to the internal resistance of the input source (RTEG), the TEG operation at the MPP will be achieved. Hence, defining the RTEG as a reference value and Rin as a feedback variable for a closed‐loop controller, the backstepping non‐linear controller is developed for input resistance control of the boost DC–DC converter. Owing to the non‐linear nature of the error variable in the input resistance control of the converters, conventional linear controllers cannot guarantee the system's closed‐loop stability within an extensive operational range. However, despite changes in generator's open‐circuit voltage (VOC) and RTEG, the designed closed‐loop controller can successfully stabilize the thermoelectric converter in different operational conditions. Considering the Lyapunov theorem and the Barbalat lemma, the asymptotic stability of the backstepping controller is proved. During the steady‐state operation, the actual values of the VOC and RTEG are updated periodically by the measurement of the converter input voltage/current values. To verify the functionality of the designed control method, PC‐based simulations are carried out in MATLAB/Simulink software. Moreover, by using TMS320F28335 digital signal processor from Texas Instruments and a simple thermoelectric simulator, the experimental response of the proposed controller is evaluated in dynamic and steady‐state conditions. The developed closed‐loop system can track the MPP of a TEG with zero steady‐state error, regardless of uncertain parameter variations.