Background: Olive is one of the world's most popular trees, primarily recognized for its seed-rich oil with numerous health benefits and high nutritive value. While polyphenols are the primary constituents responsible for these health benefits, several other valuable components remain in olive waste, which has been relatively underexplored. These waste products encompass the seed (stone), pomace, oil mill wastewater, leaves, and olive tree pruning. Scope and approach: This study introduces the application of metabolomics, an evolving technology known for its comprehensive analysis of food product composition, to address the underexplored aspects for enhancing agricultural traits, disease resistance, biotic interaction, and quality control purposes in olive trees. Meanwhile, we focus on metabolomics applications for enhancing the quality of olive byproducts, their analysis, processing, and valorization aspects. It outlines the utilization of various mass spectrometry (MS) and nuclear magnetic resonance (NMR-based) metabolomics technologies to better capitalize on these rather considered waste products. Key findings and conclusions: The review concludes by summarizing the significant findings and contributions in the literature. It highlights the impact of agricultural practices, tree origin, and diseases, such as olive quick decline syndrome, on the olive metabolome and their relevance for quality control (QC) purposes. Furthermore, it emphasizes the groundbreaking aspect of the review, which introduces metabolomics applications in the study of olive plant endophyte interactions and their effects on the olive metabolome. The potential for identifying key metabolite markers within olive byproducts is presented, which can drive future efforts to capitalize on these waste materials for valorization purposes in various food and industrial sectors.