Photosynthesis measurements are traditionally taken under steady-state conditions. However, leaves in crop fields experience frequent fluctuations in light and take time to respond. This slow response reduces the efficiency of carbon assimilation. Low to high light transitions require photosynthetic induction, including the activation of Rubisco and opening of stomata, while high to low light transitions require relaxation of dissipative energy processes collectively known as non-photochemical quenching (NPQ). Previous attempts to assess the impact of these delays on net carbon assimilation have used simplified models of crop canopies, limiting the accuracy of predictions. Here we use ray tracing to predict the spatial and temporal dynamics of lighting of a rendered mature soybean canopy to review the relative importance of these delays on net cumulative assimilation over the course of both a sunny and a cloudy summer day. Combined limitations result in a 13 % reduction in crop carbon assimilation on both sunny and cloudy days, with induction more important on cloudy than sunny days. Genetic variation in NPQ relaxation rates and photosynthetic induction in parental lines of a soybean nested association mapping (NAM) population were assessed. Short-term NPQ relaxation (<30 min) showed little variation across the NAM lines, but substantial variation was found in speeds of photosynthetic induction, attributable to Rubisco activation. Over the course of a sunny and an intermittently cloudy day these would translate to substantial differences in total crop carbon assimilation. These findings suggest an unexplored potential for breeding improved photosynthetic potential in our major crops.