Endophytic fungi live asymptomatically inside vegetal tissues, and such uncommon habitat contributes to their exceptional chemical diversity. Isolating natural products from endophytic fungi could fail due to silent biosynthetic gene clusters under ordinary in vitro culture conditions, and co‐culturing has been assayed to trigger their metabolism. We carried out single and dual cultures with 13 endophyte strains isolated from Euphorbia umbellata leaves. Multivariate statistics applied to untargeted metabolomics compared the chemical profiles of all endophyte cultures. PCA analysis guided the selection of the Aspergillus pseudonomiae J1 ‐ Porogramme brasiliensis J9 dual culture for its most significant chemical differentiation: Five compounds were putatively annotated in the J1‐J9 culture according to UHPLC‐HRMS data, kojic acid, haliclonol and its diastereoisomer, caffeic acid, and 2‐(3,4‐dihydroxyphenyl)acetaldehyde. Analysis by PLS‐DA using VIP score showed that kojic acid displayed the most significative importance in discriminating single and dual J1‐J9 cultures.