The industrial processing water of fruit and vegetables has raised serious environmental concerns due to the presence of many important bioactive compounds being disposed in the wastewater. Bioactive compounds have great potential for the food industry to optimize their process and to recover these compounds in order to develop value‐added products and to reduce environmental impacts. However, to achieve this goal, some challenges need to be addressed such as safety assurance, technology request, product regulations, cost effectiveness, and customer factors. Therefore, this review aims to summarize the recent advances of bioactive compounds recovery and the current challenges in wastewater from fruit and vegetable processing industry, including fruit and beverage, soybean by‐products, starch and edible oil industry. Moreover, future direction for novel and green technology of bioactive compounds recovery are discussed, and a prospect of bioactive compounds reuse and sustainable development is proposed.