This study uncovered the impacts of microwave (MW) treatments compared to conventional pasteurization (TP) on the quality of functional citrus–maqui beverages, with added sucrose or stevia. The influence of these thermal treatments on the microbiological burden and phytochemical composition was determined by processing under two MW power levels (600 W and 800 W) and TP at 85 °C for 15 s for 60 days at room temperature (20 °C). The results indicated that, beyond the microbiological quality achieved in the juices treated by both MW and TP technology, there were no differences among the treatments regarding the stability of vitamin C, anthocyanin, and flavanone concentrations. However, anthocyanins were more stable in those beverages with sucrose added, rendering a better red color. Besides, all treatments ensured microbiological stability throughout the entire storage time. In conclusion, MW treatment could be considered as an alternative to TP, which ensures microbial safety, protecting functional compounds associated with health effects.