Stable isotope ratio analysis of carbon (δ¹³C) and hydrogen (δ²H) in vanillin has become a valuable tool for differentiating natural vanilla from synthetic or biosynthetic alternatives and for tracing its geographical origins. However, increasingly sophisticated fraud techniques necessitate ongoing refinement of analytical methods to ensure accurate detection. This study advanced the field by investigating minor volatile organic compounds as potential biomarkers for identifying botanical and geographical origins of vanilla products. Vanilla pods from the two main vanilla species, V. planifolia and V. tahitensis, were investigated using GC-MS/MS to analyze their aromatic profile and GC-C/Py-IRMS to determine compound-specific isotope ratios, providing, for the first time, detailed and authentic isotopic and aromatic profiles. Additionally, the potential natural presence of ethyl vanillin and its corresponding glucoside precursors—molecules commonly used as synthetic vanilla-scented fragrance agents in various foods and industrial products—was explored using UHPLC-HRMS. These findings contribute to robust methods for verifying vanilla authenticity, addressing flavor complexity and isotopic composition, and enhancing the detection of adulteration in vanilla-flavored products.