The standard static gravimetric method was used to determine moisture desorption isotherms (MDIs) of two onion varieties (Goudami and Galmi Violet) at 30 °C, 45 °C and 60 °C in the water activity ranging from 0.055 to 0.83. The combined effects of temperature and water activity on the antioxidant activities of the onion varieties were also studied. GAB, Oswin, Smith and BET equations were tested to fit the experimental data. The net isosteric heat of sorption was calculated. Equilibrium moisture content (EMC), total phenolic content (TPC) and antiradical activity were also measured. The isotherm and the EMC vary significantly with the onion variety and drying temperature, irrespective of water activity (aw). Desorption isotherms were best described by the GAB model. The maximum net isosteric heats for Galmi Violet (32.58 kJ mol−1) were greater than those of Goudami (23.50 kJ mol−1) at each EMC. The TPC and antiradical activity of the Galmi Violet were significantly (P ≤ 0.05) higher than that of the Goudami at all investigated temperatures and water activities.