The increasing demand for natural ingredients in cosmetics raises new challenges for the characterization of highly complex natural extracts and the production of standardized extracts. Metabolomics has spread in a variety of research areas with great success for metabolite identification, product discrimination, and the control of quality, authenticity and adulteration. This review aims to present recent trends in the development of metabolomics tools and their potential to address new issues in natural cosmetics for more effective selection and control of natural ingredients. The current sources of natural ingredients used in skincare products are summarized. The actual metabolomics approaches are delineated, encompassing the pivotal steps of metabolomic workflow from sample extraction and metabolite identification to data mining and statistical analysis. Outlined are diverse cosmeceutical activities, ranging from antioxidant effectiveness and anti-inflammatory potential to rejuvenating properties, ultraviolet radiation protection, and the brightening attributes inherent in natural extracts. Finally, we presented the contributions of metabolomics to the quality assessment of natural cosmetics ingredients by identification of bioactive compounds, dereplication of bio-sourced ingredients, quality and safety assessment of extracts, authentication, and traceability, and the detection of adulteration. This review presents systematic approaches to studying the complex phytochemical mixtures found in natural ingredients, linking analytical techniques to biological assay systems, and thereby opening new opportunities for discovering active principles and assisting in the production of standardized compositions.