Root nodules can present a diverse bacterial community that contributes to plant growth. However, this bacterial community may vary among different plant species and their response to soil contamination, such as the application of composted tannery sludge (CTS) and Cr contamination. In this study, we assessed the bacterial community in nodules of cowpea and lima bean grown in soils with low and high rates of Cr-rich CTS. Bulk soil samples and nodules from cowpea and lima bean were collected for assessing the bacterial community by high-throughput sequencing. The bacterial diversity and the proportion of specialist bacterial species in the nodules of cowpea were higher than the lima bean. However, the bacterial diversity of the nodule was not influenced by CTS and Cr rate. The microbiome of the nodules was dominated by Proteobacteria (97.6%), followed by Actinobacteria (1.1%), and Firmicutes (0.4%). The dominant bacterial group in the nodules was Bradyrhizobium, accounting for >90% of the sequences. The functional prediction showed 26 groups, with the core functions represented by chemoheterotrophy (32.3%), followed by aerobic chemoheterotrophy (32%), nitrification (12.7%), and ammonia oxidation (11.2%). This study revealed specific differences in the nodule microbiome between the two plants species and, although suggested that the nodule microbiome was not affected by the CTS application, the functional prediction data showed that the treatments with Cr-rich CTS increased the abundance of sequences affiliated to aerobic ammonia oxidation and nitrification in the nodules. •The nodule bacterial diversity was not influenced by composted tannery sludge and Cr.•The nodule microbiome is different between cowpea and lima bean.•Bradyrhizobium dominates the nodule microbiome of cowpea and lima bean.