Background <p>Arbuscular mycorrhizal fungi (AMF) form symbioses with crops, enhancing nutrient uptake and stress tolerance. However, their responses to agronomic practices such as cover cropping and microbial grain inoculation remain poorly understood under field conditions. For maize, one of the world’s most important crops, it is still unclear how these management strategies influence AMF colonization, diversity, and community composition across growth stages and seasons, and whether they ultimately affect yield.</p> Results <p>We investigated maize root AMF colonization and community structure under cover cropping and microbial inoculation in two subsequent years with field rotation. In the first year, AMF colonization and richness followed a clear temporal pattern, peaking at the vegetative stage and declining toward maturity, while no seasonality was observed in the second year. These patterns likely reflected differences in environmental conditions (weather, soil fertility) between the field rotations. Contrary to expectations, cover crops did not enhance AMF colonization. The AMF species used for maize grain inoculation were also part of the resident community and colonized roots, being most abundant in the drier season, yet inoculation did not increase overall colonization. Shannon diversity was unaffected by crop growth stage but declined under both cover cropping and inoculation, indicating moderate changes in community composition rather than dominance by single taxa. Multivariate analyses showed that cover crops modified community composition in one year, though responses of individual taxa were limited. Despite these shifts, neither cover cropping nor inoculation consistently improved maize yield. The highest yields occurred in non-inoculated plots, with cover crops supporting productivity only in the wetter year and reducing it under stress.</p> Conclusions <p>AMF colonization and community composition in maize were driven by crop phenology and environmental conditions, whereas cover cropping and inoculation did not consistently enhance yield. These treatments modulated AMF diversity and composition in ways that may promote soil resilience under changing climatic conditions. Aligning AMF- and cover crop–based practices with site-specific environments can support more sustainable maize production.</p> Graphical abstract <p></p>