The Capsicum genus has many commercial and pharmaceutical applications. Its fruits are commonly used to provide flavour and remove insipidity in foods, but they are also bioactive and have health benefits. The bioproducts of Capsicum peppers can have antioxidant, weight-controlling, antidiabetic, anti-inflammatory, skin photoprotective, antinociceptive and cardioprotective properties. The remarkable functionality of these fruits is not related solely to capsaicinoids, but to their entire chemical profile of specialised metabolites. Chilli peppers have a large repertoire of bioactive compounds, including carotenoids, polyphenols and volatile organic compounds. The qualitative and quantitative profiles of these compounds within peppers are strongly influenced by the species, cultivar and variety, and the biotic and abiotic stressors experienced during growth. The dynamics within each chemical class are complex and, although the carotenoid profile can easily be predicted during ripening, the flavonoids vary over a wide range depending on the variety and cultivar. Knowing the chemical profile of these bioproducts and their dynamics is fundamental to developing bioproducts, exploring the potential applications of Capsicum and determining the best harvesting and post-harvesting methods.