Foods that are widely consumed and accepted have had a lot of ingredients added to them which may enhance consumer’s health. Whey is a byproduct in the manufacture of cheese or curd and is widely used in different beverage formulations, due to its nutritional importance. In this context, a mango-based functional whey drink, added with omega-3-rich chia seeds, was de veloped. Different treatments of beverage were as follows: untreated control beverage (T0), application of chemicals (T1), pasteurization (T2), and microwave heating (at 4 different time lengths: T3, T4, T5, and T6). Beverages were analyzed for physiochemical, microbiological, and sensorial changes, during the 90 days of storage. Chemical analysis of chia seeds before incorporation in beverages revealed a high nutritional profile of chia seeds, especially the presence of essential fatty acids. Significant variation in color parameters of the beverage was observed as a result of treatments and storage, with optimum values observed for T3. A decrease in pH and an increase in acidity during storage for all treatments were evident, with the most significant results for microwave treatment for longer time periods. The total plate count of the beverage was the highest (2.36 ± 0.1 CFU/ml) for control, followed by chemically treated (2.17 ± 0.1 CFU/ml) and lowest in microwave-treated (0.98 ± 0.1 CFU/ml) at the start of the experiment, and this total plate count was found to be increasing in all treatments during storage. Total solids were increased and soluble solids were decreased during longer microwave treatments and also during storage of all treatments. The most acceptable treatment T3 (85 ml whey, 2 g chia seed, and microwave heating for 30 sec) was further subjected to a storage study and it was observed that the sensory scores gradually decreased during the 90 days of storage. From the outcomes of the study, it was concluded that microwave treatment of the beverage for 30 sec, as compared to longer durations and chemical preservatives, was proved helpful for optimum quality retention of the formulated beverage, with minimum deteriorating effects. Thus, proper treatments of different beverage formulations, following the necessary protocols, could provide the consumers safe, healthy, and nutritious beverages.