Valorizing fruit and vegetable residues as renewable sources of bioactive compounds (BCs) is critical for advancing sustainable biotechnology. This review (i) assesses the occurrence, diversity and functionality of BCs in 20 edible plant residues; (ii) compares and classify them by botanical family and residue type; (iii) reviews and evaluates the efficiency of conventional and green extraction and characterization techniques for recovering phytochemical and isolating phenolics (e.g., flavonoids and anthocyanins), carotenoids, alkaloids, saponins, and essential oils; and (iv) examines the BCs’ environmental, medical, and industrial applications. It synthesizes current knowledge on the phytochemical potential of these crops, highlighting their role in diagnostics, biomaterials, and therapeutic platforms. Plant-derived nanomaterials, enzymes, and structural matrices are employed in regenerative medicine and biosensing. Carrot- and pumpkin-based nanoparticles accelerate wound healing through antimicrobial and antioxidant protection. Spinach leaves serve as decellularized scaffolds that mimic vascular and tissue microenvironments. Banana fibers are used in biocompatible composites and sutures, and citrus- and berry-derived polyphenols improve biosensor stability and reduce signal interference. Agro-residue valorization reduces food waste and enables innovations in medical diagnostics, regenerative medicine, and circular bioeconomy, thereby positioning plant-derived BCs as a cornerstone for sustainable biotechnology. The BCs’ concentration in fruit and vegetable residues varies broadly (e.g., total phenolics (~50–300 mg GAE/g DW), anthocyanins (~100–600 mg C3G/g DW), and flavonoids (~20–150 mg QE/g DW)), depending on the crop and extraction method. By linking quantitative food waste hotspots with phytochemical potential, the review highlights priority streams for the circular-bioeconomy interventions and outlines research directions to close current valorization gaps.