Recently, new formulations of beverages with low sugar and high bioactive compound contents are being demanded because of their association with metabolic health. However, the sweeteners’ influences on the bioactive compounds remain underexplored. In this sense, this work aims to evaluate the interactions between different bioactive compounds such as flavonoids, vitamin C, and sweeteners (sucrose, stevia, and sucralose) in a functional citrus–maqui beverage. For this purpose, the phytochemical behavior was studied, in model system solutions, during one-month storage at 4 °C. The results obtained corroborated previous descriptions of the interactions between these compounds. However, when studying the bioactives in the model solutions, the loss of flavanones in the citrus solution increased up to 29%, while anthocyanin losses decreased to 27%. The vitamin C losses ranged from 100% (beverage) to 46% (ascorbic acid solution). Regardless, an influence of the sweeteners was observed. Sucrose reduced the anthocyanin and flavanone losses in both model solutions and the beverage, while sucralose increased flavanone loss. Finally, all sweeteners increased vitamin C degradation (up to 75%) when compared to the model solution. In conclusion, sweeteners added to beverages should be taken into account, depending on the bioactive compounds that should be preserved during storage.