High protein content in cowpea (Vigna unguiculata (L.) Walp.) is considered as major advantage for its use in nutritional components. In this way, an experiment was conducted to investigate the effect of cropping system, site, and nitrogen fertilization on cowpea crude protein. The study comprised of three cropping systems (Maize-cowpea rotation, monocropping cowpea and intercropped cowpea), three sites (Potchefstroom, Taung, and Rustenburg, South Africa) and two rates of nitrogen fertilizers applied in kg ha -1 at each site (0 and 20 at Potchefstroom, 0 and 17 at Rustenburg, 0 and 23 at Taung). Moreover, a factorial experiment randomized in complete block design with three replications was conducted during 2011/12 and 2012/13 planting seasons. The protein content was determined from green leaves harvested before flowering, immature green pods and seeds during reproductive stage and maturity. Results showed that cropping system had significant effect on cowpea leaf protein content (P < 0.05). Intercropped cowpea significantly gave higher leaf protein (26.7% more) content than rotational cowpea. Cowpea planted at Taung had significantly higher leaf protein (30.1% more) content as compared to cowpea planted at other sites. Application of nitrogen fertilizer contributed to higher protein content of immature pods. Moreover, cowpea protein content differs among the different locations due to different soil types and climatic conditions.