For one of Canada’s most important regions of crop production—the prairies—it’s uncertain if cover crops can be successfully integrated into rotations; if so, will soil nitrogen (N) cycling be influenced to benefit main crops? To address these gaps, we compared a crop rotation with cover crops (CC) vs. without cover crops (LR) from 2018 to 2021 in Saskatoon, SK. The main crops were grown in sequence of wheat–canola–potato–pea; the cover crops included red clover, berseem clover/oat mix, fall rye, and a brassica cover. Yield and aboveground biomass were collected each year and analyzed to determine crop yield and N use efficiency (NUE). Soil N availability was monitored in various ways, that is, by assessing pre-plant soil nitrate, soil inorganic N (SIN) supply rate, and potentially mineralizable N (PMN). We found that the influence on soil N dynamics was restricted to the non-growing season where cover crops reduced SIN supply rate and nitrate content compared to the conventional practice without cover crops. Yet, rotations with vs. without cover crop did not differ in crop NUEs, yields, or in-season N dynamics. We found some evidence that diversifying rotations with cover crops may help the system to function more like perennial systems in terms of regulating N in the long run; but had limited impact during the three years studied. To ensure that cover crops are effective and functional on the prairies, innovative design approaches are needed to adapt cover crops to reach soil health goals under prairie conditions.