The by-products generated from the processing of fruits and vegetables (F&V) largely are underutilized and discarded as organic waste. These organic wastes that include seeds, pulp, skin, rinds, etc., are potential sources of bioactive compounds that have health imparting benefits. The recovery of bioactive compounds from agro-waste by recycling them to generate functional food products is of increasing interest. However, the sensitivity of these compounds to external factors restricts their utility and bioavailability. In this regard, the current review analyses various emerging technologies for the extraction of bioactives from organic wastes. The review mainly aims to discuss the basic principle of extraction for extraction techniques viz. supercritical fluid extraction, subcritical water extraction, ultrasonic-assisted extraction, microwave-assisted extraction, and pulsed electric field extraction. It provides insights into the strengths of microencapsulation techniques adopted for protecting sensitive compounds. Additionally, it outlines the possible functional food products that could be developed by utilizing components of agricultural by-products. The valorization of wastes can be an effective driver for accomplishing food security goals.