In addition to providing pigmentation to facilitate plant reproduction, flavonoid and betalain metabolites have important functions in plant tolerance to abiotic and biotic stresses. Flavonoids are ubiquitous in land plants, and the biosynthetic pathway is thought to have arisen during the period when plants were emerging onto the land around 500 million years ago. Flavonoids have been demonstrated to assist in tolerance to a wide range of stresses, and their production can be induced by cold, high light, nutrient deprivation, UV light, desiccation, salinity, senescence, metal toxicity, and pest and pathogen attack. Betalains are thought to be a much more recent acquisition by plants, as their occurrence is limited to the core Caryophyllales. As with flavonoids, a range of stress-tolerance functions for red betalain pigments have been proposed; however, their production in response to elevated salinity is of particular note. In this article, we review aspects of these pathways of much current interest: the possible mechanisms of flavonoids and betalains in providing abiotic stress tolerance and recent advances in our understanding of the transcriptional regulation that controls the induction of their biosynthetic pathways in relation to stress.