The destructive maize late wilt disease (LWD) has heavy economic implications in highly infected areas such as Israel, Egypt, and Spain. The disease outbreaks occur near the harvest, leading to total yield loss in severe cases. Crop rotation has long been known as an effective means to reduce plant diseases. Indeed, agricultural soil conservation practices that can promote beneficial soil and root fungi have become increasingly important. Such methods may have a bioprotective effect against Magnaporthiopsis maydis, the LWD causal agent. In this two-year study, we tested the role of crop rotation of maize with either wheat or clover and the influence of minimum tillage in restricting LWD. In the first experiment, wheat and clover were grown in pots with LWD infected soil in a greenhouse over a full winter growth period. These cultivations were harvested in the spring, and each pot’s group was split into two subgroups that underwent different land processing practices. The pots were sown with LWD-sensitive maize cultivar and tested over a whole growth period against control soils without crop rotation or soil with commercial mycorrhizal preparation. The maize crop rotation with wheat without tillage achieved prominent higher growth indices than the control and the clover crop cycle. Statistically significant improvement was measured in the non-tillage wheat soil pots in sprout height 22 days after sowing, in the healthy plants at the season’s end (day 77), and in shoot and cob wet weight (compared to the control). This growth promotion was accompanied by a 5.8-fold decrease in pathogen DNA in the plant stems. The tillage in the wheat-maize growth sequence resulted in similar results with improved shoot wet-weight throughout the season. In contrast, when maize was grown after clover, the tillage reduced this parameter. The addition of commercial mycorrhizal preparation to the soil resulted in higher growth measures than the control but was less efficient than the wheat crop cycle. These results were supported by a subsequent similar experiment that relied on soil taken from commercial wheat or clover fields. Here too, the wheat-maize growth cycle (without permanent effect for the tillage) achieved the best results and improved the plants’ growth parameters and immunity against LWD and lowered pathogen levels. In conclusion, the results of this study suggest that wheat and perhaps other crops yet to be inspected, together with the adjusted tillage system, may provide plants with better defense against the LWD pathogen.