Abstract Background and Aims: Agroecology practices can induce profound changes in soil inevitably influencing soil biological properties and soil functioning. However, we still lack understanding of how soil biodiversity responds to agroecology practices and to what extent such practices, alone or combined, can be beneficial for soil functioning. Understanding soil biological activities under different agroecology practices is important for predicting carbon cycling in agroecosystems. Methods: By taking advantage of a long-term agricultural experimental research station in France, we monitored soil microbes, nematodes and soil respiration over three years in response to agroecology practices that varied in the rate of nitrogen (N) fertilization (low vs high), the tillage type (deep vs reduced), and the crop residue management (retain vs removal). Results: Shifting from conventional to agroecology practices had strong effects on microbial biomass, nematode community and soil respiration. Reduced N and reduced tillage increased microbial biomass carbon, bacterivore and fungivore density. Perennial biomass crop decreased total nematode and herbivore density, but increased microbial biomass. Perennial biomass crop also significantly increased the structure and maturity indices, but decreased the plant parasite indices. Structural equation modelling showed that microbial biomass had a positive correlation with soil respiration in reduced nitrogen, reduced tillage, and residue removal treatments. Bacterivores had a positive correlation with omnivores/predators and soil respiration, while herbivores had a negative correlation with soil respiration in all the treatments. Conclusions: The different agroecological practices tested in this 4-year trial revealed the resilience of nematode communities and associated functions like CO2 respiration according to practices.