We examined the physiological responses of four soybean genotypes (KS4202, K-1639-2, ‘Jackson,’ ‘Asgrow 2703’) to soybean aphid (Aphis glycines Matsumura) feeding in reproductive stage soybeans (R1, beginning bloom). Photosynthetic capacity was evaluated by taking survey measurements at 7, 17, 24, and 28 days after aphid introduction and by measuring assimilation/internal CO2 (ACi) curves at 29 days after aphid introduction. There were no significant differences in survey measurements between the control and infested KS4202, K-1639-2, Jackson, and Asgrow 2703 plants at 7, 17, 24, and 28 days after aphid introduction. At 29 days after aphid introduction, Asgrow 2703 plants showed a significant reduction in photosynthetic capacity compared to its control plants, while infested KS4202 plants had photosynthetic rates similar to control plants, suggesting the plant’s ability to compensate for aphid feeding. Differences in gas-exchange parameters, specifically Jmax and CE, between control and infested Asgrow 2703 plants showed that soybean aphid feeding negatively impacts the carbon-linked/dark reactions, specifically rubisco activity and RuBP regeneration. This research also investigated the role of peroxidases in the defense response of soybeans to the soybean aphid. Enzyme kinetics studies documented the up-regulation of peroxidase activity for both Asgrow 2703 and KS4202 aphid-infested plants compared to their respective uninfested control plants at 24 and 28 days after aphid introduction. Peroxidase expression profiles identified differences in the isozyme profiles of aphid-infested and control plants for Asgrow 2703 and KS4202. Differences between physiological responses of infested KS4202 and Asgrow 2703, particularly temporal changes in photosynthesis activity, imply that KS4202 tolerates some impacts of soybean aphid feeding on photosynthetic integrity.