Germination is a cheap and effective bioprocessing technique used for improvement of the nutritional, physicochemical and health-promoting properties of seeds. The benefits of germination on two fonio varieties (Digitaria exilisandDigitaria iburua) have not been studied. This study investigated the nutritional and physicochemical changes in two varieties of fonio germinated for 24, 48 and 72 h at 28 °C. The antioxidant, protein and starch digestibility, functional, pasting, and thermal properties were also determined. Germination over time (24, 48, 72 h) significantly (p ≤ 0.05) increased the protein, ash, total dietary fiber, majority of the amino acids, minerals, protein digestibility, resistant starch, total phenolics and antioxidant activities while phytic acid, tannin, saponin and digestible starch contents decreased in both varieties. Germination significantly increased water and oil absorption capacity, and slightly modified pasting and thermal characteristics while bulk density decreased in both varieties. The principal component analysis revealed germination time to be the key determinant in the physicochemical, nutritional, and techno-functional characteristics of fonio rather than variety, with raw and 24 h germinated grains having similar attributes. The study established that germination improved the nutritional, antioxidant, and techno-functional properties ofDigitaria exilisandDigitaria iburua, which can serve as novel food ingredients for product development.