With the increased occurrence of climate extremes, there is an urgent need to better understand how management strategies affect the capacity of the soil microbial community to maintain its ecosystem functions (e.g. nutrient cycling). To address this issue, intact monoliths were extracted from conventional and ecological managed grasslands in three countries across Europe and exposed under common air condition (temperature and moisture) to one of three altered rain regimes (dry, wet and intermittent wet/dry) as compared to a normal regime. Subsequently, we compared the resistance and recovery of the soil microbial biomass, potential enzyme activities and community composition. The microbial community composition differed with soil management and rain regimes. Soil microbial biomass increased from the wetter to the dryer rain regime, paralleling an increase of available carbon and nutrients, suggesting low sensitivity to soil moisture reduction but nutritional limitations of soil microbes. Conversely, enzyme activities decreased with all altered rain regimes. Resistance and recovery (considering absolute distance between normal and altered rain regime) of the microbial communities depended on soil management. Conventional-intensive management showed higher resistance of two fundamental properties for nutrient cycling (i.e. bacterial biomass and extracellular enzyme activities) yet associated with more important changes in microbial community composition. This suggests an internal community reorganization promoting biomass and activity resistance. Conversely, under ecological management bacterial biomass and enzyme activities showed better recovery capacity, whereas no or very low recovery of these properties was observed under conventional management. These management effects were consistent across the three altered rain regimes investigated, indicating common factors controlling microbial communities' response to different climate-related stresses. Synthesis and applications. Our study provides experimental evidence for an important trade-off for agroecosystem management between (a) stabilizing nutrient cycling potential during an altered rain regime period at the expense of very low recovery capacity and potential long-term effect (conventional sites) and (b) promoting the capacity of the microbial community to recover its functional potential after the end of the stress (ecological sites). Thus, management based on ecologically sound principles may be the best option to sustain long-term soil functioning under climate change.