Cover crops are increasingly recognized for their role in enhancing the multifunctionality and health of soil. Previous studies have focused largely on the effects of cover crop residues and have overlooked the impacts of living cover crops on the soil biochemical processes and nutrient cycling. The aim of this study is to bridge this gap by examining the effects of different types of living cover crops, such as legumes, grass, and their mixtures, on the soil nutrients and microbial communities. We conducted a field experiment in northeastern China using an Alfisol and intercropped cover crops with maize. During the growing season, we characterized microbial biomass and community structure using phospholipid fatty acid (PLFA) analysis and assessed microbial activity through enzyme activities related to carbon (C), nitrogen (N) and phosphorus (P). Additionally, we employed the enzyme vector model to evaluate potential microbial metabolic limitations. Compared with the control plots without cover crops, the legume treatment significantly increased dissolved organic carbon (DOC) and available nitrogen, particularly altering the microbial community structure during the maize growth stages. This change shifted the microbial functional group ratios towards enhanced C acquisition by soil microbes, indicating alleviated microbial C limitation in legume treatment. In contrast, the grass treatment maintained the soil organic carbon (SOC) and total nitrogen (TN) levels, and increased the total microbial biomass at the later growth stage. Compared with those in the other treatments, the biomass of bacterial groups in the grass treatment was more responsive, and the activities of the C, N and P enzymes were higher. Furthermore, the mixture treatment merged the benefits of both the legume and grass cover crops, enhancing both DOC and available N contents and maintaining SOC and TN levels. The mixture treatment significantly affected the microbial community structure without altering microbial nutrient limitations. Thus, the mixture treatment is recommended for application in cover crop-maize intercropping systems. In conclusion, our study captured the temporal dynamic shifts in the microbial functional groups associated with different microbial life strategies from intercropping different types of living cover crops with maize. This research refines our understanding of the role of cover crops in supporting belowground ecosystems and highlights the importance of living mulch in sustainable agricultural management.