Mercury (Hg²⁺) is a natural element present in foods such as fish, water and soil. Exposure to mercury leads to severe toxic effects on the nervous, digestive, and immune systems. Here, a novel, green, and environmentally friendly fluorescent probe decorated with cysteine/MnO₂ quantum dots (Cys@MnO₂ QDs) was synthesized. This synthesis was carried out using a simple ultrasound technique with the aid of cysteine for fabricating Cys@MnO₂ QDs to estimate Hg levels in fish and water samples. In this morphological study, Cys@MnO₂ QDs were fully characterized using high‐resolution transmission electron microscopy, zeta potential analysis, fluorescence, ultraviolet–visible and infrared spectroscopy. The fluorescence of the synthesized Cys@MnO₂ QDs was significantly quenched by gradually increasing the Hg(II) concentration. The quenching mechanism based on the Hg–S bonds strengthened the utility of the Cys@MnO₂ QDs as a novel luminescent nanoprobe. The estimation of Hg was linear in the concentration range 0.7–100.0 ng mL⁻¹ with a limit of quantitation equal to 0.30 ng mL⁻¹. The Cys@MnO₂ QDs are fluorescent probes with various benefits such as speed, ease of use, cost‐ effective, and being environmentally friendly; they are easily applied in food manufacturing and for public health improvement.