This study aimed to analyze the phytochemical composition of hexane extracts from Bixa orellana L. leaves using multivariate analysis and to evaluate their antimicrobial and antioxidant activities. A total of 74 compounds were identified by Gas chromatography–mass spectrometry (GC-MS) from three cultivars, Peruvian red (PR), Peruvian green (PG), and Criolla (Cr), collected in distinct regions of Campeche, Mexico: Bécal (Be), Calkiní (Ca), and Bacabchén (Ba). The chemical classes identified included sesquiterpenes, sesquiterpenoids, alkanes, quinones, tocopherols, and sterols. Principal component analysis (PCA) indicated a clear separation of PRCa, PRBa, and CrBe from the other samples, with 86% of the total variation explained by 22 components. In PRCa (+)-ledol, (E)-β-farnesene, germacrene D, cis-β-santalene, and α-bisabolol were found abundantly. PRBa showed an abundance of β-elemene and moderate levels of caryophyllene oxide, guaiol, and γ-sitosterol. CrBe contained abundant (−)-spathulenol and phytol. The antimicrobial activity against Staphylococcus aureus showed that PRCa extracts exhibited the largest inhibition zones (23.5 ± 2.12 mm), statistically influenced by geographic origin (p = 0.0005). Conversely, PRBe and PRBa showed higher total polyphenol content and antioxidant activity, with the geographic origin × variety interaction significantly influencing these traits (p < 0.001). The findings highlight the importance of B. orellana, particularly the Peruvian red variety, as a valuable source of bioactive secondary metabolites and underscore the influence of cultivar phenotype and geographic origin on phytochemical variability and its antimicrobial and antioxidant properties.