Intensified inter-annual precipitation fluctuation has profoundly altered the structure and functioning of grassland ecosystems. However, it remains elusive how fertilisation and arbuscular mycorrhizal (AM) fungi affect plant communities under a variable precipitation regime. We tested the interactive effects of inter-annual precipitation fluctuation, nutrient addition (nitrogen, N and phosphorus, P) and suppression of AM fungi on aboveground net primary productivity (ANPP) and the species composition of plant community of a desert steppe for two consecutive years (2019 and 2020). Our study demonstrated that inter-annual precipitation fluctuation had a greater impact on ANPP and the species composition of plant community than N and P addition and AM fungi, suggesting that the impacts of fertilisation and AM fungi varied by year and may be difficult to predict over time. In a normal year (2019), N and P inputs altered the ANPP and the species composition of plant community via enhancing the biomass and dominance of annual species but had few impacts on the same parameters in a dry year (2020). AM fungi had only a minimal effect on plant communities across the two years. P input alone slightly enhanced plant species richness and diversity. Our results indicate that plant community responses to nutrient enrichment and AM fungi could be changed by inter-annual precipitation fluctuation and that precipitation is a key factor affecting plant communities in desert steppe.