Soybean (Glycine max (L.) Merr.) is the most important protein crop globally, with its cultivation area in Europe on the increase. To investigate how alternative tillage systems affect soybean growth, yield performance, and nitrogen fixation capacity in the early conversion period from conventional tillage to conservation and no-tillage practices, a field study was conducted in 2020 under the humid central European climatic conditions of Slovenia. A complete randomized block design with four repetitions was used for the three different tillage systems (conventional, conservation, and no-tillage). The results show that the majority of the studied soybean growth parameters (e.g., plant density, nodes per plant, and shoot and root dry matter) and the yield components (e.g., pods per plant, and 100-seed mass) were greatest for the reference conventional tillage system. The conventional system also showed significantly greater dry nodule mass (p < 0.01) and proportion of large-sized nodules (>4 mm) on both the tap root (p < 0.05) and the lateral roots (p < 0.001). A positive linear correlation between nitrogen content and nodule production in the roots also suggested increased nitrogen fixation for the conventional system. The less intensive conservation and no-tillage systems resulted in significantly greater soil compaction, which negatively affected early plant establishment and resulted in significantly decreased plant densities. Despite the large differences in plant stands and individual plant performances, no significant differences were seen for dry seed yields between these tillage systems. Dry seed yields for the conventional and conservation systems were 4.54 and 4.48 t ha−1, respectively, with only minor (non-significant) yield reduction for the no-tillage system, at 4.0 t ha−1. These data show that soybean cultivation in the early transition period to less intensive tillage systems have no major yield losses under these less suitable agro-climatic conditions if correct crop and weed management measures are implemented.