Understanding how water availability affects different caatinga passionfruit accessions (Passiflora cincinnata Mast.) and their drought tolerance is crucial for successful cultivation in semi-arid environments. Additionally, assessing the impact of this stress on arbuscular mycorrhizal fungi (AMF) communities' structure and dynamics is also essential. A greenhouse experiment was conducted with the purpose of identifying tolerant and sensitive P. cincinnata accessions under drought stress and how the water availability would affect AMF communities, which were taxonomically identified based on morphological characters. Results show that water availability influenced height, stem diameter, total chlorophyll, dry and fresh shoot biomass, fresh root biomass, leaf area, number of leaves and tendrils, and root/shoot ratio of accessions of P. cincinnata. However, water availability did not influence root dry biomass, only the identity of P. cincinnata accessions differed from each other. In the PCA-based ranking, based on the morpho-descriptors traits, and on the indices of drought stress tolerance, accessions 01 and 48 were considered tolerant and sensitive to drought, respectively. The abundance of glomerospores and the AMF richness are not influenced by the factors studied, but water availability has increased the frequency of mycorrhizal colonization, diversity, and evenness of AMF species, in addition to reducing its dominance. AMF communities’ composition was modulated by P. cincinnata accessions and by water availability. Utilizing morpho-agronomic traits, it becomes feasible to differentiate P. cincinnata accessions exhibiting tolerance and sensitivity to drought stress. Particular emphasis is placed on fresh and dry shoot biomass, leaf area, and height, each contributing approximately 12% to these outcomes. Changes on the composition of AMF communities after imposition of water deficit suggest that some AMF species may show some drought tolerance and that preferences for P. cincinnata genotypes may exist.