The peels of many fruits are rich sources of nutrients, although they are not commonly consumed. If they are properly decontaminated, they can be used as healthy food ingredients reducing food waste. The objective was to apply thermosonication processes to kiwi peel and evaluate the impact on Listeria innocua survival (a non-pathogenic surrogate of L. monocytogenes) and key nutrients and quality indicators: proteins, fibers, minerals (Ca, K, Mg, Na, and P), chlorophylls, and phenolic contents. Kiwi peels were artificially inoculated with L. innocua and thermal and thermosonication treatments were performed at 55 °C and 60 °C for 30 and 15 min maximum, respectively. Bacteria were enumerated through treatment time, and quality indicators were assessed before and at the end of treatments. A Weibull model with a decimal reduction time (D-value) was successfully used in L. innocua survival data fits. Results showed that coupling temperature to ultrasound had a synergistic effect on bacteria inactivation with significant decreases in D-values. Thermosonication at 60 °C was the most effective in terms of protein, fiber, chlorophylls, and phenolics retention. Minerals were not significantly affected by all treatments. Applying thermosonication to kiwi peel was more effective for decontamination than thermal treatments at the same temperature while allowing the retention of healthy compounds.