In this work, the microwave drying of amaranth seeds at different temperatures has been studied. The main objective of this study is to evaluate the effect of temperature on three key variables of the drying process and viability of amaranth seeds (drying time, energy consumption, and germination rate) after drying with microwave energy. The tests were performed in a domestic microwave oven, modified for research use, at six drying temperatures (between 35 and 60 °C). For comparative purposes, the amaranth seeds were dried by forced convection of hot air in an electric oven. It was observed that an increase in the drying temperature causes a simultaneous decrease in drying time (from 378 to 126 min) and in the energy consumption (from 9.07 to 2.61 Wh g−1, and from 412.6 to 111.7 MJ kg−1 [H2O]) and cost (from $0.065 to 0.019 USD) required to dry the seeds. However, there is also an unacceptable decrease (from ∼85% up to 23%) in the germination rate of the seeds with the drying temperature. In order to ensure the amaranth seeds’ viability after the drying process, it is necessary to employ lower drying temperatures-i.e., between 35 and 40 °C. Moreover, drying of amaranth seeds with microwave energy at 40 °C proved to be a faster and more effective method than convective drying by reducing drying time by 22% (from 336 min to 261 min) and energy consumption by 74% (from 928.4 to 274.0 MJ kg−1 [H2O]) without significantly affecting their viability.