Abstract Passiflora cincinnata Mast. or Caatinga passion fruit is widely cultivated in the northeastern semi-arid regions of Goiás, Minas Gerais, and Bahia. The system of cultivation and field management of the Passiflora species affects the physicochemical quality of its fruits. In this study, we evaluated the chemical and physico-chemical characteristics of the fruits of 2 progenies (CPEF2220 and CBAF2334) of P. cincinnata species using the vertical and horizontal trellis system. Fruits were collected from the plants at their physiological maturation stage and tested for the fruit skin color and texture and the pH, total soluble solids, titratable acidity, pulp acidity ratio, and the contents of flavonoids, anthocyanins, and polyphenols in the seedless fruit pulp. The experimental design was completely randomized in a 2 x 2 factorial scheme (progenies x conduction system) performed in 3 replications using 4 plants in each. The analysis of variance and the means were compared using the Tukey’s test at 5% probability. The results revealed that the CBAF2334 fruits presented with greener pigments and greater flavonoids. The fruits were characterized by their green color with some yellowish nuances and a low color saturation in both the progenies. The conduction system was not found to affect the physical and physicochemical characteristics as well as the anthocyanin and polyphenol contents of the studied species. The fruits of plants cultivated on vertical trellis presented with 56.73% more flavonoid content than those cultivated on horizontal trellis.