Coconut inflorescence sap, traditionally called as neera, is a natural and healthy drink obtained by tapping the unopened immature spadix of coconut. The sap tapped by using the device coco-sap chiller, developed by ICAR-Central Plantation Crops Research Institute, is called Kalparasa®. The shelf life of the sap after extraction is 2–3 h in atmospheric condition. Farmer producer companies and palm sap processing industries require suitable preservation techniques to maintain the physico-chemical properties of the coconut sap. Hence, the effect of microwave power level (600 and 900 W) and exposure time (30, 60, 90, and 120 s) on the physico-chemical properties of Kalparasa stored under refrigerated conditions was investigated. The physico-chemical properties of microwave-treated Kalparasa including pH, TSS, titratable acidity, ascorbic acid, total sugar, reducing sugar, and polyphenols were analysed at 1, 3, 5, 7, 9, 12, and 16 days after storage. The results reveal that the microwave treatment and storage period had a significant effect (P < 0.001) on the physico-chemical properties of Kalparasa. Furthermore, it was deduced that a combination of high power (900 W) and exposure time (120 s) maintains the physico-chemical quality of Kalparasa up to 16 days of storage under refrigerated conditions.