Changes in soil micronutrient availability may have adverse consequences on grassland productivity, yet it’s still largely unclear how concurrent human practices, such as fertilization and mowing, affect micronutrient cycling in the plant-soil systems. Here, we measured six essential micronutrient (Fe, Mn, Cu, Zn, Co and Mo) contents in both plant pool (separated as aboveground plant parts, litter, and belowground roots) at the community level and soil pool (0−10 cm depth) after 12-year consecutive nitrogen (N) addition (0, 2, 10, and 50 g N m−2 year−1) and mowing in a typical steppe of the Mongolian Plateau. The results show that (i) medium-N (10 g m−2 year−1) and high-N (50 g m−2 year−1) addition rates significantly increased contents of soil-available Fe (+310.0%, averaging across the two N addition rates), Mn (+149.2%), Co (+123.6%) and Mo (+73.9%) irrespective of mowing treatment, whereas these addition treatments usually decreased contents of soil total Fe (−8.9%), Mn (−21.6%), Cu (−15.9%), Zn (−19.5%), Co (−16.4%) and Mo (−34.7%). (ii) Contents of Fe in aboveground plant parts, litter, and roots significantly decreased, whereas plant Mn increased with N addition. Contents of above ground plant Cu, Zn, Co, and Mo significantly decreased at high-N addition rate, whereas contents of micronutrients in roots and litters, except for Fe, generally increased with N addition. Moreover, the total amount of micronutrients in the plant pool (contents × biomass) significantly increased at the medium-N addition rate but decreased at the high-N addition rate. All N addition rates significantly enlarged the pool of litter micronutrients, and roots could hold more micronutrients under N addition, especially combined with mowing treatment. Importantly, although mowing could regulate the effects of N addition on variables (i) and (ii), the effects were weaker overall than those of N addition. (iii) Changes in root micronutrients, except for Mn, could explain corresponding changes in plant micronutrients (R2: 0.19−0.56, all p < 0.01), and significant linear correlations were also observed between soil-available Fe and Fe in plant and roots. Aboveground plant Mn was significantly correlated with soil-available Mn, while Co and Mo in roots were also significantly correlated with soil-available Co and Mo. These results indicate that soil micronutrient supply capacity may decrease due to a decrease in total micronutrient contents after long-term N addition and mowing. They also suggest that different magnitude responses of soil micronutrients in plants (i.e., litters, roots) and soil should be considered when comprehensively examining nutrient cycling in grassland ecosystems.