Millets are important food crops in food systems and application of physical treatments could improve the functional properties of millet-based products. Therefore, we investigated the effect of heat and γ-irradiation treatments on the pasting, rheological, and microbial load of whole and dehulled millets (sorghum, foxtail millet, and pearl millet). Moreover, similarity in treatment effect was evaluated by principal component analysis (PCA). The results revealed the significant ( p < 0.05) decrease in pasting properties of whole and dehulled millets, except for pasting temperature (71.03 to 74.88 °C). Likewise, significantly ( p < 0.05) decreased tendency was observed for all rheological properties, except for phase angle (0.05 to 0.30°) and yield point (13 to 5089). Samples showed a significant ( p < 0.05) reduction in fungal growth (89.75 × 104 to 4.46 × 104 CFU/g) compared to control (110.30 × 104 CFU/g). Moreover, samples individually formed 3 clusters (clusters 1: sorghum, 2: pearl millet, and 3: foxtail millet) based on pasting properties, which was confirmed by PCA. Therefore, the findings concluded that the effect of heat and γ-irradiation would be necessary to decrease pasting, rheological, and no microbial growth characteristics of dehulled and whole millets for the development of specific millet-based food products.