Intercropping and fertilization practices are increasingly promoted as ecological alternatives to improve soil health and crop productivity. This work examined their combined effects on soil microbial communities and onion yield over two growing seasons. The aim of this study was to assess how different intercropping systems combined with organic and mineral fertilization influence soil microbial communities and onion performance. Treatments included onion monoculture and intercropping with carrot, pepper or fennel, under compost and NPK fertilization, arranged in a randomized block design. Soil analyses focused on bacterial, fungal and actinomycetes loads, microbial biomass carbon (MBC), and their relationship with onion yield. Results indicated that growing season, fertilization, and intercropping, as well as their interactions, had significant effects on all microbial parameters and yield (p < 0.001). Compost application led to the highest microbial stimulation, increasing bacterial populations by 42%, fungal counts by 33%, actinomycetes by 45%, and MBC by 32%, compared to the unfertilized control. Carrot intercropping further enhanced soil activity, raising actinomycetes by 48% and MBC by 35%. This cropping system also improved onion performance, with yield rising from 2.5 kg/plant in the control to 5.4 kg/plant under compost treatments and 5.1 kg/plant with carrot intercropping, highlighting the positive link between microbial enhancement and productivity. Moderate positive correlations were observed between microbial parameters and yield, particularly for bacteria (R² = 0.27) and actinomycetes (R² = 0.20). These findings emphasize the potential of integrating organic fertilization with strategic intercropping to enhance soil biological functioning and promote sustainable onion production.