The soil engineering function of legumes in natural ecosystems is paramount but associated solely with soil nitrogen (N) subsidies, ignoring concomitant biotic interactions such as competitive or inhibitory effects and exchange between mycorrhizas and rhizobia. We aim to (1) disentangle legume effects on plant community composition, and plant and soil N and phosphorus (P) concentrations, separating the effects of N subsidies from other legume effects; (2) estimate effects of mycorrhizal-rhizobial interactions on nutrient acquisition modes of plants co-existing with legumes. We compared plant community structure and plant nutrition modes in micro-sites in a Caucasian alpine tundra ecosystem that were either: (1) dominated by legumes in symbiosis with N-fixing rhizobia (‘N-fixing legumes'), (2) dominated by legumes without symbiosis with rhizobia (‘not N-fixing legumes'), or dominated by non-legumes and either (3) unfertilized (‘controls') or (4) experimentally fertilized. Fertilization and the presence of N-fixing legumes affected the ecosystem similarly: soil was enriched with plant-available N compared to controls and sites dominated by a not N-fixing legume. Also, N turnover pathways and plant nutrition modes were strongly affected by the latter site types, as indicated by 5–10% higher plant tissue N concentration, altered soil and plant d15N, more than 4-fold reduced lichen amounts, 2.5-fold increased litter accumulation and doubling of aboveground biomass of non-legume plants. Vascular plant community composition was affected by the presence of legumes in a similar way regardless of whether they fixed N, suggesting that other factors overrode the N subsidy effects. Shading and microclimate changes in sites dominated by both types of legumes are possible explanatory factors. Both tissue N and d15N of non-legume plants near legumes were affected by interactions of mycorrhizal type and site type (without legumes, dominated by N-fixing, or not N-fixing legume), suggesting an important role of plant mycorrhizal status for adjusting nutrition mode to the legume presence. We conclude that N-fixing legumes play an engineering role in natural plant communities, but their role goes much beyond N fixation. Plant mycorrhizal status defines the way plants adjust their nutrition mode to the presence of legumes