Honey is one of the most popular natural sweet substances. From a chemical point of view, it could be defined as a natural food mainly composed of sugars and water (W), along with other minor constituents such as minerals, vitamins, amino acids, organic acids, flavonoids, and other phenolic compounds and aromatic substances. Its composition is particularly variable, depending on its botanical and geographical origins. In addition to beneficial components, certain honeys may contain natural toxic compounds derived from specific botanical sources, which can pose health risks if consumed in high quantities. The stability of these bioactive and potentially toxic compounds, particularly in relation to storage conditions and the effects of processing, is crucial for ensuring honey’s nutritional value and safety. Analytical methods such as high-performance liquid chromatography (HPLC), gas chromatography–mass spectrometry (GC-MS), inductively coupled plasma mass spectrometry (ICP-MS), and nuclear magnetic resonance (NMR) spectroscopy are commonly employed for both identifying honey’s major compounds and detecting contaminants. The aim of this chapter is to describe the principal families of compounds present in honey, review the stability of these compounds, and discuss the analytical methods employed for their analysis, as well as their utility in discriminating honeys according to their origin and quality.