Seed quality is considered as a major agricultural issue with respect to food and non-food uses, biodiversity preservation and environmental protection. Germination efficiency and seed vigor are key factors to ensure correct plant production and yield. Germination can be limited by seed dormancy and/or suboptimal environmental conditions. In addition, seed viability is a fundamental trait to consider in the management of genetic resources and market chain. Seed quality is largely determined by the accumulation of various storage compounds including specialized metabolites (SMs) with protective functions. Therefore, a comprehensive investigation of seed SMs is of paramount importance. During the last years, developing multiomics approaches has provided a wealth of data highlighting the key biological functions and major molecular/metabolic hubs of seed specialized metabolites. This chapter will give an updated overview of the biodiversity of these metabolites and the regulatory networks that control their production and storage. We will also discuss the spatial distribution and structure/function relationships of these SMs. We will focus on the following four major groups detected in seeds, phenylpropanoids (more than about 10,000 compounds), alkaloids (about 20,000 compounds), sulfur-containing compounds (e.g., glucosinolates), and terpenoids (more than 40,000 compounds).