Thermal processing of pulse crops influences the type and levels of prebiotic carbohydrates present. Pulses such as common bean and chickpea are rich sources of prebiotic carbohydrates, including sugar alcohols (SAs), raffinose family oligosaccharides (RFOs), fructooligosaccharides (FOSs), resistant starch (RS), and amylose. This study determined the changes in prebiotic carbohydrate concentrations of seven common bean and two chickpea market classes after thermal processing (cooking, cooling, and reheating). A 100-g serving of common bean provides 0.7 to 10.6 mg of SAs, 3.9 to 5.2 g of RFOs, 57 to 143 mg of FOSs, 2.6 to 3.9 g of RS, and 25 to 33 g of amylose; cooling and reheating reduced RFOs but increased SAs, FOSs, and RS in many cases. A 100-g serving of chickpea (cooked at 90°C for 4 hr) provides 1.2 to 1.7 g of SAs, 2.5 to 3.2 g of RFOs, 26 to 43 mg of FOSs, 3.6 to 5.3 g of RS, and 24 to 30 g of amylose; cooling and reheating reduced SAs and RFOs but increased FOSs, RS, and amylose concentrations. Processing methods change the nutritional quality of pulse crops by changing the type and quantity of prebiotic carbohydrates.