Amaranth grain is gluten free and has high levels of protein. The total mineral content of amaranth grain is generally greater than that observed in conventional grains. This study focused on amaranth milling with three different mills (burr mill, roller mill, and nutrimill), with three corrugations (0.002 in., 0.005 in. and 0.010 in.) and three moisture levels (10%, 20%, and 24% w.b.). The following physical properties were measured in the grain: seed dimension, one thousand seed weight, and moisture content before and after tempering. The following physical properties were measured in the flour: mean particle size, bulk density, color, angle of repose, moisture content, thermal conductivity, thermal diffusivity, and specific heat capacity. Results show that one thousand seed weight (W1000) of the amaranth grains increased linearly with an increase in moisture content, from 0.75 to 0.88 grams. The mean particle size of the flour increased with an increase in moisture content. It was observed that changes in the physical properties correlated with moisture content. The results of this study give understanding of changes that ought to be considered in the processing and handling of amaranth flour. These results will be relevant when incorporating amaranth flour into gluten-free food products.