Cropping systems with legumes play key roles in farming systems in sub-Saharan Africa. However, how commonly legume associations perform in low input-systems is not well-known. Here, we studied four legume species used in three systems in rotation with upland rice, i.e., groundnut monocropping, sorghum–cowpea intercropping, and velvet bean–crotalaria intercropping, in two fertilization managements on the previous rice, i.e., manure alone or complemented with mineral fertilization. Legume suitability was assessed using rhizobial and mycorrhizal colonization rates, plant biomass production, shoot N and P content, and biological N2 fixation based on their d15N natural abundance. Shoot and root biomasses varied significantly between legume species and were positively correlated with nodule number (r = 0.49 and 0.74, p-value < 0.05 and <0.001, respectively) and the amount of fixed N (r = 0.73 and 0.50, p-value < 0.001 and <0.05, respectively). The proportion of plant N derived from N2 fixation also varied significantly between species, with a higher percentage for velvet bean (66%), compared to the other three species (50 to 60%). Legume roots were weakly colonized by AM fungi, with similar levels between species. Overall, fertilization management did not significantly impact legume biomass, symbioses, or N2 fixation, yet the organo-mineral fertilization significantly increased legume shoot P content. The lack of effect of mineral fertilization on N2 fixation and biomass could be due to other nutrient deficiencies (Ca, Mg, micronutrients), which can hamper symbioses with rhizobia and mycorrhizae.