Passion fruit is one of the main crops produced in the irrigated areas of Northeastern Brazil. However, soil salinization in this region has limited its productivity. This work aimed to compare the effects of saline stress on three populations of passion fruit (Passiflora edulis Sims, P. mucronata Lam. and the interspecific hybrid P. edulis x P. mucronata) using physiological, anatomical, nutritional, agronomic traits and application of near-infrared spectroscopy (NIBS). Plants were grown on sterile washed sand and irrigated with a nutrient solution with or without NaCI (0 or 150 mM) in a completely randomized design with eight replicates. Most of the physiological traits, such as transpiration, stomatal conductance, net photosynthetic rate, chlorophyll content and leaf osmotic potential, were negatively affected by the saline stress. There was also a negative effect for the majority of anatomical traits evaluated in the presence of NaCl, except the stomatal density and upper epidermal thickness. The NaC1 also induced changes in uptake of macro- and micronutrients and decreased plant growth, fresh shoot and root weights, and dry shoot weight. Based on the principal component analysis (PCA), 18 informative traits were identified for the discrimination of the passion fruit population for saline stress. P. mucronata exhibited better salt tolerance in comparison with the other populations, especially with higher values for root traits, a lower accumulation of sodium in the leaves, and maintenance of photosynthesis, conductance and stomatal functionality. Near-infrared spectrophotometry (NIBS) allowed the separation of the parental Passifiora populations submitted to the saline treatment, opening the possibility of validating its use for screening passion fruit genotypes for tolerance of salinity. Breeding for salt tolerance in passion fruit is feasible using wild species such as P. mucronata.