Food colourants are widely used additives classified as either synthetic or natural. In recent years, consumers have increasingly favoured natural options, considering them safer and potentially beneficial due to their nutritional properties. This study examined the effects of a natural food colourant, commercially known as Vegan Red (RVEG), on zebrafish embryonic development. Its impact was compared with cochineal red E120, of animal origin, and the synthetic dye E124, which are associated with hyperactivity in children and allergies. Shield stage embryos were exposed for 72 h and then examined using a multidisciplinary approach to assess the effects on conventional toxicity endpoints, such as survival, hatching rate, heart rate, genotoxicity, and behavioural interferences, including the impact on muscle ultrastructure. The results demonstrated that RVEG, as well as E120, do not affect hatching, heart rate, and motility parameters. However, RVEG moderately alters skeletal muscle organisation and, more relevant, the expression of the , and genes. Based on standard toxicity parameters, the findings indicated that RVEG is less toxic than E124 and E120, but that the alterations induced in gene expression and muscle anatomy raise safety concerns.