The regional agroecological conditions, specific to the Transylvanian Plain, are favorable to soybean crops, but microclimate changes related to global warming have imposed the need for agrotechnical adaptive measures in order to maintain the level of soybean yield. In this study, we consider the effect of two soil tillage systems, the seeding rate, as well as the fertilizer dosage and time of application on the yield and quality of soybean crops. A multifactorial experiment was carried out through the A × B × C × D − R: 3 × 2 × 3 × 3 − 2 formula, where A represents the year (a1, 2017; a2, 2018; and a3, 2019); B represents the soil tillage system (b1, conventional tillage with mouldboard plough; b2, reduced tillage with chisel cultivator); C represents the fertilizer variants (c1, unfertilized; c2, one single rate of fertilization: 40 kg ha−1 of nitrogen + 40 kg ha−1 of phosphorus; and c3, two rates of fertilization: 40 kg ha−1 of nitrogen + 40 kg ha−1 of phosphorus (at sowing) + 46 kg ha−1 of nitrogen at V3 stage); D represents the seeding rate (1 = 45 germinating grains (gg) m−2; d2 = 55 gg m−2; and d3 = 65 gg m−2); and R represents the replicates (r1 = the first and r2 = the second). Tillage had no effect, the climate specific of the years and fertilization affected the yield and the quality parameters. Regarding the soybean yield, it reacted favorably to a higher seeding rate (55–65 gg m−2) and two rates of fertilization. The qualitative characteristics of soybeans are affected by the fertilization rates applied to the crop, which influence the protein and fiber content in the soybean grains. Higher values of protein content were recorded with a reduced tillage system, i.e., 38.90 g kg−1 DM in the variant with one single rate of fertilization at a seeding rate of 45 gg per m−2 and 38.72 g kg−1 DM in the variant with two fertilizations at a seeding rate of 65 gg m−2.