Passion fruit woodiness disease, caused by the Cowpea aphid-borne mosaic virus (CABMV), is one of the leading phytosanitary challenges of passion fruit production. Passiflora cincinnata has been recognized for its potential in genetic improvement due to its highest resistance to CABMV and other phytopathogens. Metabolomic and histological alterations of P. cincinnata infected with CABMV were evaluated and searched for differential responses during the asymptomatic or symptomatic infection phases to correlate them with the mechanisms of metabolic defense. The metabolites of infected plants were analyzed by liquid chromatography-mass spectrometry. Based on the metabolomic profile, the times of infection were grouped into early or late infection phases. The metabolites related to CABMV infection were classified as alkaloids, saponins, phospholipids and acids. This study can assist agricultural institutions or farms in the early diagnosis and correct management of CABMV infection and contribute to the genetic improvement of the Passiflora genus against this disease.