Olive fruit fly, Bactrocera oleae (Rossi) (Diptera: Tephritidae), is the most important olive pest, with major economic importance in olive production worldwide. Different olive cultivars exhibit different propensities to fruit fly infestation and the causes are still unclear. Here, we want to disclose the potential role of olive-associated endophytes in conferring such susceptibility differences. Accordingly, the endophytic microbial composition of infested and non-infested fruits from cultivars Madural (susceptible to olive fly) and Cobrançosa (less susceptible) were studied. A culture-dependent approach was used, the isolates being identified by sequencing of their internal transcribed spacer (for fungi) and 16S rRNA gene regions (for bacteria). Overall, there was a larger consortium of bacteria associated with olives than fungi. The bacterial communities were predominantly composed of Proteobacteria and Actinobacteria phyla, while the fungal isolates belonged to the Ascomycota and Basidiomycota. Both host cultivar and level of fly infestation had a negligible effect on fungal and bacterial community composition. Despite this, a clear positive association of microbial consortia with the resistant cultivar (Kocuria sp., Actinobacterium sp., Rhodococcus sp., Pseudomonas citronellolis, Aspergillus flavus, Cladosporium sp., and Meristemomycetes arctostaphylos) and non-infested fruits (Kocuria sp., Stereum sp., and Vishniacozyma victoria) was found. Their functional roles in host cultivar susceptibility/resistance to the fruit fly is a topic that requires further studies.