Application of herbicides and other agro-chemicals used in agriculture affects the vital functions and population dynamics of soil microorganisms. Soil microbial population was assessed in 30 days interval up to 90 days in mango and citrus orchards. Among the treatments, intercropping of greengram-peagreengram recorded higher bacterial population (21.7 x 106cfu/g), was followed by intercropping of cowpea-pea-cowpea (19.5x106 cfu/g) at 90 days after spraying. It was found that the highest fungi population was recorded in intercropping of greengram-pea-greengram combined with herbicide application treatment (14.4 x 103 cfu/g). Similarly, higher actinomycetes population was observed in intercropping of greengram-pea-greengram treatment (8.2 x 103cfu/g) followed by intercropping of cowpea-pea-cowpea (7.3 x 103cfu/g) in mango orchard. In citrus field, highest bacterial population was observed in intercropping of greengram-pea-greengram treatment (21.3 x 106cfu/g).This was followed by intercropping of cowpea-pea-cowpea (18.4 x 106 cfu/g). The maximum fungi population (14.8 x 103cfu/g) was observed in cowpea-pea-cowpea treatment and maximum actinomycetes (8.4 x 103 cfu/g) population was recorded in intercropping of greengram-pea-greengram treatment. Basal respiration was significantly more in treatments of intercropping systems. Among the treatments, intercropping of greengram-pea-greengram treatment (193 mg/kg of CO2-C) had more basal respiration rate during Kharif season in mango orchard. Similar trends were observed in citrus orchard.