This chapter presents a comprehensive protocol for the extraction, derivatization, and GC-MS analysis of metabolites in fresh and fried vegetables, focusing on sweet potato (Ipomoea batatas) and broccoli (Brassica oleracea var. italica). These vegetables are nutritionally important and increasingly incorporated into processed products through vacuum and deep-frying techniques. However, these thermal processes significantly alter their metabolite profiles, particularly sugars, amino acids, and organic acids. The protocol includes optimized sample preparation, Bligh-Dyer extraction, and dual-step derivatization (methoximation followed by silylation using MSTFA) to enhance volatility and detectability in GC-MS. It also accounts for matrix-specific challenges, including lipid interference in fried samples and moisture variability. Applications of this method include nutritional profiling, detection of process-induced transformations, and quality control in vegetable-based snacks. This workflow provides a practical, adaptable guide for researchers conducting high-resolution metabolite analysis in plant-derived food matrices.