Under natural conditions, cold and freezing stress is one of the detrimental factors plants face during their life cycle. For acclimatization, adaptation, and defense, plants accumulate specialized metabolites such as flavonoids, phenolics, alkaloids, saponins, and tannins. Identification of metabolites is especially important to study the impact and resilience toward stress conditions. The present chapter briefly describes metabolite profiling from a plant sample, including sample harvesting, metabolite extraction, identification, and quantification. The first and most crucial step in metabolomics is sample preparation (sample harvesting, drying, metabolite extraction, and preparation for analysis), which impacts the accuracy of the result and largely depends on analytical tools and the class of metabolites. Liquid solvent extraction of alkaloids, saponins, and tannins has been discussed. Advanced extraction methods for volatile compounds, like headspace analysis and solid-phase microextraction (SPME), are also reviewed. We also discussed liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-mass spectrometry (GC-MS) based protocols for metabolite profiling.