Gluten free cookies were prepared from raw and germinated amaranth grain flour. The chemical, functional and pasting properties of raw and germinated amaranth flour were studied. Germination decreased fat from 6.68 g to 4.7 g/100 g and carbohydrate 62.41 g–60.70 g/100 g while an increase was noticed in protein from 15.05 g to 16.5 g/100 g, total dietary fibre from 9.52 g to 12.9 g/100 g and antioxidant activity from 10.23 g to 14.71 g/100 g, respectively. Further, functional properties were improved on germination. Pasting properties values were decreased with germination. The gluten-free cookies were evaluated for their physical, textural, colour, antioxidant activity, total dietary fibre and sensory attributes. Raw amaranth flour cookies showed the highest spread ratio, followed by germinated amaranth flour and wheat flour cookies. Germinated amaranth flour cookies require minimum snap force. Germinated amaranth cookies exhibited highest antioxidant activity (21.43 g/100 g) and total dietary fibre (13.97 g/100 g) as compared to raw amaranth and wheat flour cookies. The overall results showed that the cookies with acceptable quality and improved nutrition could be prepared from germinated amaranth flour.