Consumer interest in food quality and safety has shifted over time, as consumers increasingly prefer minimally processed items. As a result, numerous non-thermal approaches have been implemented due to their potential to preserve the nutritional profile of products along with lengthening their storability. Microwaving, a green processing technique, volumetrically heats the product because of the interactions developed between charged ions, polar water molecules of foodstuff and the incoming electromagnetic waves. The study was mapped out to investigate the effect of microwave exposure time (60, 90 and 120 s) at fixed power (1000 W) and frequency (2450 MHz) on physicochemical properties, phytochemical constituents, antioxidant potential and microbial counts of lemon cordial stored at refrigerated temperature (4 ± 2 °C). The mentioned parameters were analyzed after an interval of 30–90 days. Statistical findings illustrated a highly significant (p ≤ 0.01) impact of microwave treatment and storage on titratable acidity, pH, total soluble solids, total phenolic contents, total flavonoids contents, antioxidant potential and total plate count. Sample microwaved for 120 s showed the highest pH values (2.45 ± 0.050), total soluble solids (56.68 ± 2.612 °B) and antioxidant activity (1212.03 ± 716.5 µg—equivalent of ascorbic acid per 100 mL of cordial); meanwhile, it exhibited the lowest total plate counts (1.75 ± 0.144 Log 10 CFU/mL). Therefore, microwaving can be suggested as a suitable alternate to traditional pasteurization techniques as well as to chemical preservatives.