Fungal endophytes are known to produce secondary metabolites. The synthesis of vanillin and its precursors have never been clearly elucidated. Given fungi can produce such metabolites, it is speculated that fungal endophytes in vanilla could be contributing to vanillin and its precursors. An investigation was thus carried to find whether fungal endophytes are present in Vanilla planifolia. Additionally, vanilla flavor varies across cultivation regions; hence, the distribution of endophytes across regions was also assessed and found to differ. The metabolic changes brought by the fungi on vanillin and its precursors in vanilla pods were also evaluated. Out of 434 isolated fungal endophytes, two candidates emerged: Pestalotiopsis microspora and Diaporthe phaseolorum. However, P. microspora increased the most the absolute amounts (quantified by 1H NMR in μmol/g DW green pods) of vanillin (37.0 × 10−3), vanillyl alcohol (100.0 × 10−3), vanillic acid (9.2 × 10−3), and p-hydroxybenzoic acid (87.9 × 10−3) when cultured on green pod-based media. Given the physical proximity of fungi inside pods, endophytic biotransformation may contribute to the complexity of vanilla flavors.