Pigeon pea (Cajanus cajan (L.) Millsp.), a potential legume as an economical source of protein, is commonly cultivated in tropical and subtropical regions of the world. Therefore, pigeon pea may be potentially used as a substitute to improve the nutritional profile of foods. In the present study, the effect of substitution of whole wheat flour (WWF) with 20% and 40% pigeon pea flour (PPF) on the nutritional properties, color profiles, and starch and protein digestibility of chapati was investigated. The results showed that PPF had higher protein content but less carbohydrate than WWF. The protein content of chapati substituted with 20% and 40% PPF increased by 1.18 and 1.34 times, respectively, compared to WWF chapati, along with a marked decrease in carbohydrate content. Analyses further revealed an increase in the lightness and yellowness and a decrease in the redness of the chapati. Furthermore, glucose release from chapati with 20% and 40% PPF under simulated digestion was attenuated, corresponding to decreased hydrolysis and a predicted glycemic index. In the 40% PPF chapati, a significant reduction in slowly digestible starch (SDS) with increased resistant starch (RS) proportions was achieved without altering the effect on rapidly digestible starch (RDS). In addition, the level of amino-group residues was markedly elevated in 20% and 40% PPF substituted chapati compared to WWF chapati. These findings suggest that PPF can serve as a promising plant-based alternative ingredient to improve the nutrient value of chapati by reducing starch and increasing protein digestibility.