Biochar and arbuscular mycorrhizal fungi (AMF) are agricultural interventions adopted by farmers to improve the growth of crops in nutrient-deficient acidic soil, which relatively influence the biological properties in the rhizosphere. This greenhouse study investigated the changes in prokaryotic diversity in the rhizosphere of cacao plants grown in acidic soil with AMF and bamboo biochar (BB) for 15 months under nursery conditions. Metagenomic analysis of the V3-V4 region of the 16S rRNA gene of the rhizosphere with AMF, 15% BB, and AMF + 15% BB revealed that the addition of AMF and BB reduced the sample's diversity, but the treatments increased the overall plant growth. Of all Operational Taxonomic Units (OTUs) recovered, the top three abundant phyla in the treated soils were: Proteobacteria, Acidobacteria, and Actinobacteria. The relative abundances of Proteobacteria and Acidobacteria increased with the treatments, whereas that of Actinobacteria was decreased. Biochar increased the unclassified genera under Order Acidobacteriales and Chromatiales. In contrast, AMF increased the abundance of an unclassified genus under Order Xanthomonadales. The genus Rhodoplanes was the most dominant in AMF + 15% BB-treated soil with a relative abundance of 9.4%. The four samples shared only 4.9% of the total OTUs; apparently, the microbial communities across samples were separated and distinct. Most of the increased genera have been reported to play essential roles in nutrient cycling, which may contribute to cacao growth promotion.