This study synthesized equimolar ZnO–CdO composite nanoparticles using an ultrasonic-assisted method with citrus lemon extract as a bio-functionalizing agent. X-ray diffraction and microscopy revealed that bio-functionalization reduced crystallite size from 45.90 to 28.80 nm while improving particle dispersion and homogeneity. Optical analysis showed bandgap narrowing from 3.15 to 2.94 eV. Photocatalytic testing under UV irradiation demonstrated that citrus-functionalized nanoparticles achieved 96% degradation of methylene blue, crystal violet, and tetrazine dyes, surpassing conventional samples (87%). Degradation followed pseudo-first-order kinetics. Results indicate that citrus-mediated bio-functionalization offers a sustainable approach for enhancing photocatalytic efficiency in aqueous pollutant remediation applications.