Phaseolus vulgaris (common bean) is an agronomic important legume crop native to America, where two centres of genetic diversification (GD) are recognised, one in Mesoamerica and the other in the south Andes. Mesoamerican bean accessions have preferential and more efficient nodulation with Rhizobium etli strains carrying the allele nodC type-α, which is predominant in soils of Mesoamerica. It was previously demonstrated that the host nuclear factor NF-YC1, which is involved in nodule formation and rhizobial infection, contributes to this preferential selection and enhances nodulation in the domesticated accession NAG12 from Mesoamerica. Here, we show that both domesticated and wild Mesoamerican beans exhibit higher nodulation performance with a nodC type-α than with a nodC type-δ strain. Transcripts of NF-YC1 significantly increased in roots of these accessions 24 h post-inoculation (hpi) with the nodC type-α strain. On the other hand, accessions from the Andean GD centre formed a higher number of nodules with a strain carrying the nodC type-δ, which is predominant in Andean soils. However, NF-YC1 transcript levels did not exhibit significant changes in Andean accessions upon inoculation with the nodC type-δ strain, at least at 24 hpi. RNA interference (RNAi)-mediated gene silencing of NF-YC1 in the domesticated Andean accession Alubia showed that NF-YC1 or a closely related member of this family is required for nodule formation and bacterial infection, in agreement with observations in Mesoamerican common beans. Isolation and sequencing of the full-length ORF of NF-YC1 from Alubia revealed that it was identical to the sequence previously identified in the Mesoamerican accession NAG12. Interestingly, overexpression of NF-YC1 had a negative impact on nodule formation in the Alubia accession, independently of the R. etli lineage. Our findings suggest that transcriptional and functional variation of NF-YC1 occurs among genetically diverse bean accessions, which might positively or negatively contribute to the fine-tuning mechanisms that regulate nodule formation in the common bean–R. etli symbiosis.