Over the past 10 years, knowledge about several aspects of fruit metabolism has been greatly improved. Notably, high-throughput metabolomic technologies have allowed quantifying metabolite levels across various biological processes, and identifying the genes that underly fruit development and ripening. This Special Issue is designed to exemplify the current use of metabolomics studies of temperate and tropical fruit for basic research as well as practical applications. It includes articles about different aspects of fruit biochemical phenotyping, fruit metabolism before and after harvest, including primary and specialized metabolisms, and bioactive compounds involved in growth and environmental responses. The effect of genotype, stages of development or fruit tissue on metabolomic profiles and corresponding metabolism regulations are addressed, as well as the combination of other omics with metabolomics for fruit metabolism studies. The growth and ripening of fruit are multifaceted and highly regulated developmental processes which yield colorful and flavorful tissues for organisms that consume and disperse the seeds therein [1]. Fruits are economically essential and vital for human nutrition and health owing to their content in sugars, organic acids, pigments, volatiles and other nutraceutical compounds [2,3], the metabolisms of which have been widely studied (e.g., [4-6]). The shift from single-metabolite analyses to analytical platforms that provide information on hundreds of metabolites has allowed researchers to better describe the links both within metabolites and between metabolism and important agronomic-associated traits. Metabolomics has permitted the identification of changes in the chemical composition of transgenic plants, mutants or populations and has allowed for identifying genomic regions associated with metabolite traits of agronomical value in model fruit species such as tomato and strawberry [7]. Tomato metabolomic studies have been numerous in the past decade [8,9] and have allowed the development of a comprehensive understanding of primary and specialized metabolism pathways and their interplay during fruit growth and development, and in diverse environmental conditions. The number of teams involved in, and of articles published on, fruit metabolomics has been regularly and progressively increasing. Searching for articles in the Web of Science core collection for metabolomic(s) or metabolome, and fruit in the last decade (Figure 1) revealed an increment from