GC-MS is one of the most widely used analytical instruments for metabolite profiling of different biological samples. There are many methodologies involving different types of metabolite extraction and sample preparation strategies available in published literature. For horticultural crops, GC-MS has been used to analyze both volatile and semi/nonvolatile compounds. To analyze volatile compounds, GC-MS is undeniably the most suitable analytical platform as it allows direct detection of volatile compounds within the samples. However, semi/nonvolatile metabolites can also be analyzed in horticultural crops using GC-MS and many efforts have been made to develop and optimize different derivatization protocols. This book chapter covers a detailed description of different methodologies available for the analysis of both volatile and nonvolatile metabolites in different fruit and horticultural products using both targeted and untargeted approaches by GC-MS. In addition to methodologies, key considerations that need to be considered while performing GC-MS-based metabolite profiling will also be outlined.