Capsaicinoids are acid amides of C9–C11 branched-chain fatty acids and vanillylamine and constitute important chemical compounds of Capsicum annuum together with their non-pungent analogs (capsinoids) which have an impressive list of health benefit properties (i.e., analgesia, anti-obesity, thermogenic, cardiovascular, gastrointestinal, antioxidant, anti-bacterial, anti-virulence, anti-inflamatory, anti-diabetic, inhibits angiogenesis, and improves glucose metabolism). In this review, the state of art on how capsaicinoids are affected by different pre- and postharvest factors is discussed together with their biological activity. For instance, high light intensity and heat treatments may reduce capsaicinoid content in fruits probably due to the loss of activity of capsaicin synthase (CS) and phenylalanine ammonia lyase (PAL). The pungency in peppers varies also with environment, genotype or cultivar, node position, fruiting and maturity stages, nitrogen and potassium contents. As the fruit mature, capsaicinoid levels increase. Fruits from the second node tend to have higher accumulation of pungency than those of other positions and the pungency decreases linearly as the node position increase. Sodium hydroxide treatment reduces the pungency of pepper fruit as it hydrolyzes and modifies one of the features (vanillyl group, the acid-amide linkage and alkyl side chain) of capsaicin molecule. Salt and water stress increase PAL and capsaicin synthase activity and increase the capsaicinoid accumulation in fruit, by negatively regulating peroxidase activity at appropriate levels. Future research must be directed in better understanding the changes of capsinoids during pre and post-harvest management, the causal drivers of the loss of activity of the aminotransferase gene (pAMT) and if possible, studies with genetically modified sweet peppers with functional pAMT. Available data provided in this review can be used in different agricultural programs related to developing new cultivars with specific pungency levels. The contents of capsaicinoids and capsinoids in both fresh fruits and marketed products are also of remarkable importance considering the preferences of certain niches in market where higher added-value products might be commercialized.