Finger millet is a cereal grain which is superior to wheat and rice in terms of dietary fibre, minerals, and micronutrients. Fermentation is one of the oldest methods of food processing, and it has been used to ferment cereal grains such as finger millet (FM) for centuries. The aim of this study was to investigate the impact of spontaneous fermentation (SF) on mineral content, functional, thermo-pasting, and microstructural properties of light- and dark-brown FM flours. Spontaneous fermentation exhibited a significant increase in the macro-minerals and micro-minerals of FM flours. In terms of functional properties, SF decreased the packed bulk density and swelling capacity, and it increased the water/oil absorption capacity of both FM flours. Spontaneous fermentation had no effect on the cold paste viscosity of FM flours. However, significant decreases from 421.61 to 265.33 cP and 320.67 to 253.67 cP were observed in the cooked paste viscosity of light- and dark-brown FM flours, respectively. Moreover, SF induced alterations in the thermal properties of FM flours as increments in gelatinisation temperatures and gelatinisation enthalpy were observed. The results of pasting properties exhibited the low peak viscosities (1709.67 and 2695.67 cP), through viscosities (1349.67 and 2480.33 cP), and final viscosities (1616.33 and 2754.67 cP), along with high breakdown viscosities (360.00 and 215.33 cP) and setback viscosity (349.33 and 274.33 cP), of spontaneously fermented FM flours. Scanning electron microscopy showed that SF influenced changes in the microstructural properties of FM flours. The changes induced by SF in FM flours suggest that flours can be used in the food industry to produce weaning foods, jelly foods, and gluten-free products that are rich in minerals.