In the current work, the production of dioxolanone and meroterpene type secondary metabolites under different fermentation conditions by the endophytic fungus Phyllosticta capitalensis (isolate YCC4) isolated from the leaves of the endemic plant Persea indica has been evaluated. Different techniques, such as microparticle-enhanced culture (MPEC: bentonite, talcum powder) and surface adhesion fermentation (SAF: metallic mesh and glass wool) were applied to the culture medium. Ethyl acetate extracts from different fermentations of the isolate YCC4 were analyzed for their content and revealed the following dioxolanone derivatives: metguignardic acid (1), guignardianone C (2), ethyl guignardate (3), guignardianone D (4) and phenguignardic acid methyl ester (5), and meroterpenes: guignardone A (6) and B (7), guignarenone C (8), guignarenone B (9) and guignardone I (10). Additionally, the biological activity of extracts was tested against the aphid Myzus persicae and the root-knot nematode Meloidogyne javanica. Our study revealed significant variations in the production of the target metabolites as well as notable differences in biopesticide activity influenced by the presence of inert supports. Overall, the findings indicate that glass wool (GW) is a high-performance material to improve the production of dioxolanone derivatives. These findings underscore the significance of innovative cultivation methods such MPEC and SAF as drivers to produce valuable secondary metabolites from fungal organisms.