The inclusion of legumes in crop rotations can provide numerous benefits to crop productivity and environmental sustainability. However, these benefits have primarily been documented in systems that involve regular fertilization, limiting our understanding of legume effects under low-input or long-term unfertilized conditions. Though soybean (Glycine max L.) is one of the globally most important cultivated legumes, data on its effect on subsequent common wheat (Triticum aestivum L.) crop in low-input European systems are scarce. This study builds on long-term historically consistent trails of two rotation systems: maize-winter wheat (M-W) and maize-soybean-winter wheat (M-S-W) under rainfed conditions on a Chernozem in Serbia, maintained without fertilization for over 70 years. The aim of our work was to evaluate the effect of soybean as pre-crop on wheat yield and yield components and accumulation of Fe, Zn, Cu and Mn in grain. Over five growing seasons, the soybean pre-crop effect resulted in a grain yield increase ranging from 43% to 301%. Results showed that three-fold higher soil mineral N promoted productive tillering, spike development and grain setting in M-S-W. Two-year data on micronutrient concentrations in grain revealed significantly higher levels of Zn and Cu in M-S-W, as well as grain protein content. However, the yield dilution effect in the M-S-W rotation led to reduced levels for both Fe and Mn in one growing season. This long-term field experiment underscores the agronomic and environmental significance of soybean-based rotations, enhancing soil N fertility and carbon sequestration, and offering a sustainable solution for winter wheat production.