This review focused on the influence of environmental systems and/or factors including high tunnel, UV and visible light, fertilization, and irrigation on bioactive compounds in vegetables and fruits. Most studies reported that high tunnel reduced chicoric acid and luteolin in vegetables including lettuce and pac choi, and fruits including raspberry and tomato versus open field, although a few studies demonstrated that high tunnel did not significantly impact on the bioactive compounds. Light including UV such as photosynthetically active radiation (PAR), UV-A, and UV-B, and visible light especially red and blue light, significantly stimulated biosynthesis of anthocyanins, flavonoids, and phenolics, and promoted their contents in vegetables such as onion and spinach, and fruits for example blueberry and strawberry. The effect of fertilization including nitrogen, phosphorus, and potassium on bioactive phytochemicals (carotenoids, flavonoids, polyphenols) in vegetables (broccoli, kale) or fruits (tomato) varied among the cultivars. Water deficit usually increased anthocyanins, flavonoids, and phenolic acids in vegetables such as lettuce and red beet, and fruits including grape and pomegranate. Taken together, the bioactive compounds in vegetables and fruits in response to environmental factors were species- and varieties- dependent. The negative effect of environmental factors on bioactive compounds in vegetables and fruits can be overcome by selecting appropriate cultivars, while the positive effect can be further manipulated in horticultural production for potential consumer’s health benefits.