This study evaluated the response of soil microbial functions to the presence and placement of faba beans in crop rotations (rotation without legumes versus rotations with faba beans as the crop previous to wheat, with the faba beans sown three years before the wheat crops) combined with two tillage systems (conventional and reduced tillage). The study included 36 wheat-producing plots, and two agricultural practice types were defined: high-frequency–low-intensity (HF–LI) and low-frequency–high-intensity (LF–HI). The results demonstrated a significant increase in the total carbon and nitrogen (N) content under reduced tillage. Furthermore, the general path analysis suggested that arylamidase and β-glucosidase activities significantly affect N fluxes. The enzyme activities were modified by changing the soil’s physicochemical properties. These findings highlighted the significance of introducing legumes as the crop preceding wheat, especially when applying conventional tillage. Moreover, it was revealed that farmers’ management of these conservative practices is a leading factor in regulating soil functions. Pesticides and inorganic fertilization inputs were classified as HF–LI practices, while organic matter (OM) inputs and liming treatments were qualified as LF–HI practices. For instance, LF–HI practices (OM inputs and liming) directly and indirectly influenced the soil functions related to the N cycle, while HF–LI practices (pesticide, inorganic N fertilization, and previous crops) resulted in fewer soil function changes.