Nitrogen (N) availability under no-till intercropping systems has not been widely investigated in diverse agro-ecological regions in Limpopo Province. Two seasons of rainfed experiments were conducted during 2018/19 and 2020/21 in a 2 × 4 × 2 factorial design to measure the biological nitrogen fixation (BNF) ability of cowpea in an intercropping system with four grain sorghum cultivars at two test locations, Ofcolaco and Syferkuil, of Limpopo Province using the natural abundance technique. The cowpea nitrogen isotope composition (δ 15N‰) ranged from 0.2 ‰ to 4‰ at Ofcolaco, whereas at Syferkuil, the range was 2 ‰ to 7 ‰. The N derived from air (Ndfa) was from 35% to 92% at Ofcolaco and 4% to 70% at Syferkuil during the two cropping seasons. The amount of N2 fixed across locations and seasons ranged from 1 kg ha−1 to 71 kg ha−1. In the intercropping system, cowpea fixed more N at higher densities compared with lower densities at the two experimental sites. Biomass was significantly correlated with N accumulated by cowpea (r2 > 0.9) at all locations and across seasons. N accumulated in sole cultures was 30% more at Ofcolaco and 36% more at Syferkuil compared with binary cultures. Furthermore, the treatment combination, cowpea density, as well as cropping system, significantly affected N fixation and accumulation. For high productivity, cowpea intercrop with grain sorghum cultivar Enforcer is recommended, as both crops complemented each other when intercropped. The research should investigate further the root distribution and biomass production of sorghum and cowpea, as well as their impact on N intake.