The integration of soybean into polyspecies cropping systems is a promising approach for enhancing the overall productivity of agrocenosis. The study was conducted over two years (2024–2025) at the Field Experimental Station of the Russian State Agrarian University – Moscow Timiryazev Agricultural Academy. The aim of the study was to identify the patterns of soybean productivity and grain quality formation of under polyspecies agroecosystems to optimize cultivation technologies. The experiment was established in a randomized block design with four replications; 14 crop combination variants were studied. The main crop was soybean, variety Mageva; cereals and legumes were used for creating polyspecies crops. A significant effect of polyspecies composition on soybean productivity parameters was established (p < 0.05). Over the two-year average the maximum chlorophyll content in leaves (0.034 mg/cm2) was recorded in the “Soybean + field pea” variant at the BBCH 19 stage; the highest grain yield (3.03 t/ha) and dry matter yield (7.35 t/ha) were obtained in the “Soybean + mustard” variant; the maximum protein content in grain (43.79%) was recorded in the “Soybean + white lupine” variant. Joint sowing of soybean with mustard increased grain yield by 1.86 t/ha, while sowing with white lupin enhanced grain protein content by 5.67% compared to soybean monoculture. Joint cultivation of soybean with mustard and white lupine is an effective technique for increasing soybean yield and grain quality under Non-Chernozem zone conditions.