In vanilla, compounds that exhibit antimicrobial activity are synthesized; however, the variation in phytochemicals present in the plant structures of this species is little known, in relation to the environmental condition and the crop system. The objective of this research was to quantify the variation in phytochemicals in leaf, stem, flower, green fruit and cured fruit from two vanilla chemotypes (QI and QVI) grown in acahual (native and introduced secondary vegetation) and shade mesh systems. Vanilla chemotypes were collected during the flowering period and at harvest in four locations in the Totonacapan region, Mexico. The concentration of total phenolic compounds, total tannins, hydrolysable tannins, condensed tannins, flavonoids, saponins and triterpenes was analyzed in methanolic extracts by spectrophotometric methods. The phytochemicals accumulated at different concentrations in the vanilla plant tissues in relation to the condition of the crop management system and the chemotype. Acahual cultivation favored the concentration of total phenolic compounds, total, hydrolysable and condensed tannins, and total triterpenes, while the values obtained with shade mesh were higher in saponins. QVI accumulated the highest concentration of phytochemicals, with the exception of hydrolysable tannins that showed no statistical difference between chemotypes. The environmental condition affected the phytochemical concentration of phytochemicals in the plant structures of vanilla. Elevation was the environmental variable that most impacted the accumulation of phytochemicals, since it showed an inverse effect on the concentration of total triterpenes, total tannins and condensed tannins.