Abstract Background and Objectives To enhance the utilization of pulse ingredients, greater knowledge of the effect of infrared (IR) processing on protein and starch nutrition is needed. The current study investigated the use of tempering (20% vs. 30% moisture) with IR heating (120°C vs. 140°C) to improve the nutritional value of two commercially important pulses: green lentils and yellow peas. Findings Proximate composition remained mostly unchanged after IR heating for both pulse types. The protein's secondary structure transitioned to a state with a higher amount of random coils as IR processing conditions intensified (increase in moisture and temperature). In vitro protein digestibility (IVPD) increased from 73% to 78%−82% for green lentil and 78% to 81%−85% for yellow pea, depending on IR processing treatment. Tryptophan was the limiting amino acid in all samples. The IVPD corrected amino acid scores were not significantly altered by IR processing. The content of rapidly (RDS) and slowly (SDS) digestible starches increased, whereas that of resistance starch declined with IR processing. Conclusions The combined effect of tempering moisture and IR heat as a premilling treatment changed the protein secondary structure but did not improve the overall protein quality of the pulses. Starch digestibility was improved with IR processing. Significance and Novelty Employing tempering and IR heating techniques on pulses may be useful in food and feed applications where improved starch digestibility is desired.