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Semi‐arid grasslands on the Mongolian Plateau are expected to experience high inputs of anthropogenic reactive nitrogen in this century. It remains unclear, however, how soil organisms and nutrient cycling are directly affected by N enrichment (i.e., without mediation by plant input to soil) vs. indirectly affected via changes in plant‐related inputs to soils resulting from N enrichment. To test the direct and indirect effects of N enrichment on soil organisms (bacteria, fungi and nematodes) and their associated C and N mineralization, in 2010, we designated two subplots (with plants and without plants) in every plot of a six‐level N‐enrichment experiment established in 1999 in a semi‐arid grassland. In 2014, 4 years after subplots with and without plant were established, N enrichment had substantially altered the soil bacterial, fungal and nematode community structures due to declines in biomass or abundance whether plants had been removed or not. N enrichment also reduced the diversity of these groups (except for fungi) and the soil C mineralization rate and induced a hump‐shaped response of soil N mineralization. As expected, plant removal decreased the biomass or abundance of soil organisms and C and N mineralization rates due to declines in soil substrates or food resources. Analyses of plant‐removal‐induced changes (ratios of without‐ to with‐plant subplots) showed that micro‐organisms and C and N mineralization rates were not enhanced as N enrichment increased but that nematodes were enhanced as N enrichment increased, indicating that the effects of plant removal on soil organisms and mineralization depended on trophic level and nutrient status. Surprisingly, there was no statistical interaction between N enrichment and plant removal for most variables, indicating that plant‐related inputs did not qualitatively change the effects of N enrichment on soil organisms or mineralization. Structural equation modelling confirmed that changes in soil communities and mineralization rates were more affected by the direct effects of N enrichment (via soil acidification and increased N availability) than by plant‐related indirect effects. Our results provide insight into how future changes in N deposition and vegetation may modify below‐ground communities and processes in grassland ecosystems.