Plant pigments have a vital role in plant pollination, aesthetic appeal, and quality of the fruit. Naturally occurring major plant pigments include anthocyanins, carotenoids, and chlorophyll. In addition to their coloration, these pigments possess additional beneficial properties, which is why they are often referred to as bioactive compounds. Moreover, they exhibit strong antioxidant and antimicrobial properties. The pigments, particularly beta-carotene (a precursor to vitamin A), a type of carotenoid, are crucial for maintaining good vision. They can help reduce the risk of age-related macular degeneration and improve overall eye health. The antioxidants found in fruit pigments may improve cognitive function and reduce neurodegeneration. This review article explores the processes involved in the biosynthesis of essential pigments in fruits, emphasizing their biological significance and various applications, including effects on human health and economic value. Understanding these mechanisms can improve the color and quality of fruits, resulting in high consumer acceptance and higher market demand. The numerous benefits of plant pigments have sparked growing interest in incorporating them into our food. However, in-depth research is required to explore the biological significance of fruit pigments, as well as their role in human food and nutrition. Studies have shown that these bioactive compounds can help prevent and manage chronic degenerative diseases. Further research is necessary in both fundamental and applied areas to enhance pigment levels in fruit to a degree sufficient for disease prevention. Comprehensive research into the genetic regulation of pigment biosynthesis could illuminate pathways for enhancing pigmentation through genetic engineering or traditional breeding methods. Genome editing technologies like CRISPR could be employed to improve specific pathways related to pigment biosynthesis in fruits. Further promising opportunities for the application of these pigments beyond the food industry should be investigated, focusing on their potential contributions in cosmetics, textiles, medicine, agriculture, and other sectors.