Abstract Aims Inoculation with climate-adapted rhizobia is able to increase legume productivity in drought-prone regions of Sub-Saharan Africa. Enhanced nodulation might additionally affect plant-soil interactions and control rhizosphere carbon (C) and nitrogen (N) pools. Methods We investigated inoculation effects on nodulation and biological N₂ fixation (BNF) of Vigna unguiculata and consequent effects on C and N pools in two Namibian soils. Three treatments (Bradyrhizobium sp.1–7 inoculant, non-inoculated, N-fertilised with 50 kg N ha⁻¹) were applied in rhizoboxes at 45% and 20% maximum water holding capacity. Nodule development was photo-documented, and rhizobia-DNA sequences were identified. BNF was assessed by δ¹⁵N enrichment, and organic C and N pools were analysed in bulk and root adherent soil. Results Plant growth initially enhanced mineral N losses from the rhizosphere at flowering stage (6 weeks growth), but led to a re-increase of N, and organic C contents after ripening (10 weeks). Inoculation had no effect on nodulation and soil C and N pools, indicating that both soils contained sufficient indigenous rhizobia to allow effective nodulation. However, the inoculant strain was more competitive in establishing itself in the root nodules, depending on the local conditions, showing a need for regional adjustment of inoculation strategies. Conclusion Water stress was the main limitation for nodulation and, in combination with soil type, substantially affected rhizosphere and bulk soil C and N contents. The temporally enhanced rhizodeposition after ripening could be able to maintain soil C and N pools after legume cultivation.