Different substrates have been implemented for the production of functional beverages. To avoid the presence of pathogens, beverages have been subjected to thermal treatments, such as sterilization or pasteurization, which can interfere with the physicochemical, rheological, functional, and organoleptic properties of the final product. The objective of the present study was to evaluate the effects of heat treatment on the physicochemical properties, such as acidity, pH, total solids, density, total and reducing sugar, as well as the antioxidant activity of a beverage formulated from rice flour (RF) and coconut water (CW). Three beverage formulations were evaluated: A (2% RF; 98% CW), B (5% RF; 95% CW), and C (8% RF; 92% CW), each of which was subjected to two heat treatments: sterilized (121 °C/15 psi/15 min) or pasteurized (60 °C/60 min and subsequently 73 °C/15 s). The heat treatments increased the acidity and reducing sugars but decreased pH, total sugar, and antioxidant activity. As for the rheological properties, the mixtures were pseudoplastic fluid. The physicochemical properties from RF and CW mixtures were dependent on the heat treatment, but these can be introduced as new nondairy substrates for the elaboration of functional beverages to be consumed mainly by those lactose intolerant.