Health consciousness and the need to maintain immune system have increased the demand for fresh fruit and vegetable juices due to the presence of nutritional benefits including colorful pigments such as chlorophylls, carotenoids, and anthocyanins. Besides providing green, yellow, and red color in fruits and vegetables, these phytochemical compounds play an important role in health maintenance through their antioxidant activity. However, natural pigments have been known to be susceptible to adverse conditions including pH and temperature. Heat treatment is commonly applied in the processing of fresh juices in order to extend shelf-life. Nevertheless, thermal treatments have been reported to cause detrimental impacts on the quality of juices. Thus, non-thermal treatments such as high pressure processing (HPP) and ultraviolet (UV) light have become alternative methods to preserve the juices without high impact on nutritional and sensory characteristics. This review underlines the chlorophyll, carotenoid, and anthocyanin pigments in green, yellow, and red fresh juices obtained from several fruits and vegetables, with the influence of pH and non-thermal treatments (HPP and UV) on the color and stability of pigments in the fresh juices.