Upper canopy leaves of maize decrease the light-transmittance at middle-strata-leaves of maize and soybean canopy in maize-soybean relay-intercropping systems (MS). This affects the uptake of nutrients and distribution patterns in various plant organs of intercrop species in MS. Judicious defoliation of maize plants in MS could help to alleviate this problem and improve nutrient uptake and intercrop yields. In a two-year field experiment with MS, including the measurements of biomass production, nutrients uptake, and distribution at the organ level, and grain yields of intercrop species, maize plants were subjected to four-leaf defoliation treatments to improve the light-transmittance of maize and soybean plants. Defoliation of the topmost two-leaves (T2), four-leaves (T4), six-leaves (T6) was compared to no defoliation (T0). Compared to T0, treatment T2 improved the uptake of nitrogen (N), phosphorus (P), and potassium (K) in each plant part of maize by 23, 12, and 11% (grain), 22, 19, and 13% (straw), and 28, 14, and 18% (root), respectively. Defoliation also enhanced the uptake of N, P, and K in each plant part of soybean by 5, 5, and 10% (grain), 10, 17, and 13% (straw), and 14, 11, and 11% (root), respectively. The improved nutrient uptake in T2 increased the total biomass and its distribution in the root, straw, and grain of soybean and maize by 15 and 13%, and 21 and 15%, 20 and 14%, 7 and 10%, respectively compared to T0. On average, over two years, under T2, relay-cropped maize obtained 107% of the sole-yield, and relay-cropped soybean obtained 65% of the sole-yield. The T2 defoliation treatment also achieved the highest land equivalent ratio of 1.69 and 1.77, with a net profit of 1301.6 $ ha−1 and 1293.4 $ ha−1 in 2017 and 2018, respectively. Following the optimum defoliation treatment of maize in maize-soybean intercrops, i.e., defoliation of the topmost two-leaves, the nutrient uptake can be increased, and the nutrient partitioning over plant organs be better balanced. Optimum defoliation, therefore, enhances the productivity of maize-soybean intercropping systems.