The aim of this study was to evaluate the effects of winter cover crops (CCs) on soybean agronomic performance and their implications for different physiological groups of rhizosphere microorganisms in two sustainable production systems. The production techniques for rye, peas, and oats are well known, but their suitability as CCs for soybean (organic and low-input) production needs to be examined. After two years of trials, soybean yields among the two tested winter CCs (peas and oats (P + O) and rye (R)) were statistically significant only for P + O. The soybean yield in succession to P + O as winter CCs was 3.0 t ha−1, whereas in succession to R, it was 2.7 t ha−1, and in the control plot, it was 2.6 t ha−1. The average soybean grain protein content was in the range of 40 to 41% dry matter (DM), while the oil content ranged from 20 to 22% DM. Protein and oil content primarily depends on the selected soybean variety and it is confirmed through this study that, in the studied system, we can obtain adequate grain nutritional quality. The results indicate an increase in the abundance of total bacteria, ammonifiers, and free N2-fixing bacteria in the rhizosphere, depending on the selected CCs, and differences between the tested production systems. According to this study, winter cover crops (CCs), including peas and oats (P + O) and rye (R), can be included in crop rotation for soybean. CCs can be the answer to agro-biodiversity empowerment in less diverse soybean cropping systems, along with other benefits that CCs can provide at the level of crop rotation. In addition, in almost all aspects of the study, organic production was ahead of low input. Low input is an adequate production system if there are no opportunities for organic certification and for producers who are aware of the advantages of sustainable systems, and it can also represent a transitional path towards regenerative agriculture or organic production.