The current study is aimed at studying the effect of ultrasonication on finger millet and barnyard millet flours which were processed for 10, 15, and 20 min at a constant amplitude of 30% and 30 kHz frequency at a maximum power of 750 W and 220 V. Ultrasonication resulted in modification of functional, structural, color, thermal, and molecular interactions and bioactive properties of millet flours. Ultrasonication resulted in decrement of water absorption capacity (1.51–1.36 and 1.51–1.05 g/g), swelling power (7.68–5.34 and 5.87–4.50 g/g), and foaming stability, while an increment was observed in water solubility index (3.59–8.41% and 3.03–10.94%), oil absorption capacity (1.98–2.16 g/g and 1.93–2.07 g/g), foaming capacity (12.00–17.00% and 18.00–25.00%), and paste clarity (51.20–61.00%T and 58.50–63.60%T) in finger millet and barnyard flours. An increase in bioactive components was observed till 15 min was observed, followed by reduction on further treatment. Ultrasonication triggers cavitation, which causes cell wall fractures and subsequent breakdown, ultimately reducing particle size. The resulting particle size reduction increases the surface area, enhancing functional properties. Ultrasonication reduced the enthalpy of millet flours by disrupting amorphous regions. Concurrently, processing altered surface topography, modified functional groups, and changed crystal structure. Also, the antinutritional factors (phytates and tannins) were reduced linearly on an increase in the time period of ultrasonication. This study shows that ultrasonication improves the functional properties of finger millet and barnyard millet flours.