Essential oils (EOs) are complex chemical matrices on which whole cell biotransformations have not had much success due to their well-known antimicrobial activities. The approach in this work is to use endophytic microorganisms to increase the chemical diversification of Eupatorium buniifolium EO by biocatalysis. Three endophytic fungal strains showing ability to biotransform the EO and four of the EO main pure components, R-(+)-limonene, alpha-(-)-pinene, alpha-(+)-pinene and sabinene, were isolated from E. buniifolium plants. Two strains were characterized up to species level as Fusarium solani Eb01 and Alternaria alternata Eb03 and the third strain at genus level as Neofusicoccum sp. Eb04. The three fungi, as resting cell systems, allowed to access to three new complex volatile matrixes from E. buniifolium EO by increasing its degree of oxyfunctionalization. The robustness and biocatalytic skills of these microorganisms make them worth their inclusion within the tool-box for the generation of new valuable bioproducts from hydrocarbon monoterpene rich feedstocks.