Eupatorium tremulum is a South American shrub reported to cause cattle digestive intoxication, of which the volatile oil, mainly composed by bisabolane- and amorphane-type sesquiterpenoids, exhibits high quantitative variability. This report describes the application of chemometric tools for the identification of volatile compounds that characterize phenophasical changes in the plant. Preblooming, blooming, and postblooming specimens were paired-sampled and submitted to hydrodistillation and GC-MS analysis. Differential results were analyzed by orthogonal projection to latent structures-discriminant analysis (OPLS-DA), and the substances with different distribution in each phase were highlighted. Mean results between phases were submitted to factor analysis (FA), and correlations between the variables were demonstrated. Preblooming to blooming phase change was characterized by decreased levels of amorpha-4-en-7-ol (13) and epi-α-bisabolol (19) and increased amounts of amorpha-4,7(11)-diene (1). Blooming to postblooming change was characterized by decreases in 1, germacrene D (2), and β-bisabolene (4) and increases in 13 and 19. Finally, enhanced levels of 1, 4, and 2 reflected the change from the postblooming to the preblooming phase. FA revealed a strong correlation in the variability between the bisabolane hydrocarbons, possibly related to its common enzymatic origin. Another strong source of negative correlation showed bisabolane- and amorphane-type alcohols, on one side, and amorphane-type furans, on the other side, to occur in two alternative oxidation routes. Finally, 1 was strongly negatively correlated to its oxidized furan and ketofuran derivatives [verboccidentafuran (16) and 3-oxo-verboccidentafuran (23)] and additionally to a third compound, putatively identified as a biosynthetic intermediate between this hydrocarbon and the furans, amorpha-4,7(11)-dien-8-one (20).