A gold nanoparticle–modified copper-based metal organic framework (Au NPs@Cu-BDC) was fabricated for the electrochemical determination of cysteine (Cys-SH). The nanocomposites were characterized using different techniques such as scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy-dispersive X-ray spectroscopy (EDX), powder X-ray spectroscopy (PXRD), thermogravimetry (TGA), nitrogen adsorption–desorption isotherms, and Fourier transform infrared spectroscopy (FTIR). Formation of a new anodic peak of Cu(II)-Cys complex at + 0.43 V was used to detect Cys-SH. Cyclic and square wave voltammetric studies proved that the Au NPs enhanced the conductivity of Cu-BDC. The proposed electrode exhibited a linear range of 0.0015–10.5 μM and low detection limit of 0.0004 μM with a good sensitivity of 0.78 ± 0.01 μA μM. The as-fabricated electrode was successfully used for the estimation of Cys-SH in real samples (human plasma, urine, and saliva) with recovery % of 99–100% and RSD % of 2.7–3.6%, respectively.