Smallholder farmers need to cope with small farm sizes, low soil fertility, and risks associated with rain-fed agriculture, which resulted in low productivity. Crop diversification potentially improves yields and resource use efficiencies in these systems. Field experiments were conducted at two sites in southern Ethiopia to determine the effects of common bean (Phaseolus vulgaris L.) intercropping time and frequency on biological nitrogen fixation (BNF), nutrient uptake, and soil properties. Treatments included monocrops of maize (M) and common bean (Bn), double common bean mono crop (Bn + Bn), simultaneous (M + Bn), relay (M + BnR), and sequential common bean intercropping with maize (M + Bn + Bn). BNF by common bean under these systems was estimated BNF using the N-15 natural abundance method. Intercropping had no significant (p > 0.05) effect on BNF compared to common bean monoculture at both sites. However, there were significant differences in BNF among intercropping systems at site 1. Significantly higher BNF were obtained from M + Bn + Bn compared with M + Bn and M + BnR. Intercropping significantly (p < 0.05) increased the N and P uptakes compared to unfertilized maize monoculture at both sites, resulting in increased yields but no significant effect on nutrient use efficiencies. Significantly higher N and P uptakes were obtained from M + Bn + Bn compared to other intercropping, and significantly lower N and P uptakes were obtained from M + Bn and M + BnR. Intercropping had no significant (p > 0.05) effect on most soil properties possibly due to the short experimental duration. Therefore, nutrient management strategy is required in intercropping systems to counter the increased nutrient uptake which could cause soil depletion in the long term particularly if all biomass is removed from the field.