In this work we demonstrate that the synergistic combination of organic molecules extracted from food waste can empower different types of carboxylated gold nanoparticles (Au NPs) in removal of Cr(VI) species from both milliQ and real water solutions. In particular, chitosan extracted from shrimp’s shell and dissolved in an acidic active medium based on a 1:3 M mixture of ascorbic and citric acid allows citrate-capped Au NPs to improve their abatment efficiency from 18.4 to > 99% in milliQ and 80.6% in drinking water. When citrates are exchanged with 3-mercaptopropionic or 11-mercaptoundecanoic acids, the efficiency reaches 100% in both milliQ and drinking water. 11-mercaptoundecanoic acid is found to be the best capping agent in terms of efficiency and stability. Crossing of cyclic voltammetry and UV–Vis data enabled to define the main role of each individual component in abatment of Cr(VI). This study further advances research on the rational design of hybrid nanoparticle/polymer systems for environmental remediation, inspired by criteria of circular economy and environmental sustainability.