Abstract Traces of cadmium (Cd) have been reported in chocolate products due to growing cacao plants in soils with Cd and the ability of cacao plants to accumulate it. A strategy to minimize this uptake of Cd is by using cadmium-tolerant bacteria (CdtB) to sequester the Cd. This study was aimed to isolate and characterize CdtB associated with cacao-cultivated soils in Cundinamarca-Colombia. Thirty CdtB morphotypes were isolated and almost half of them showed the capacity to fix nitrogen, solubilize phosphates and degrade cellulose. Besides, all strains were selected for analysis of 16S rRNA sequence. The soil with the highest natural concentration of Cd (location Y3) showed higher abundance, unique morphotypes, and dominance of isolated CdtB. Pseudomona putida GB78, Pseundomona aeruginosa NB2, and Burkholderia sp. NB10 were the only morphotypes that grew on 18 up to 90 (GB78) and 140 mg Kg − 1 Cd (NB2-NB10). GB78 showed the highest Cd bioaccumulation (5.92 mg g − 1 ). Our results expand the knowledge about culturable CdtB in cacao-cultivated soils with the potential to develop soil management strategies to mitigate the uptake of Cd by cacao plants, thereby preventing the potential impact on human health, food safety, and the cacao economy.