In this investigation, a melamine electrochemical sensor has been developed by using wet‐chemically synthesized low‐dimensional aggregated nanoparticles (NPs) of ZnO‐doped Co3O4 as sensing substrate that were decorated onto flat glassy carbon electrode (GCE). The characterization of NPs such as UV‐Vis, FTIR, XRD, XPS, EDS, and FESEM was done for detailed investigations in optical, functional, structural, elemental, and morphological analyses. The ZnO‐doped Co3O4 NPs decorated GCE was used as a sensing probe to analyze the target chemical melamine in a phosphate buffer at pH 5.7 by applying differential pulse voltammetry (DPV). It exhibited good performances in terms of sensor analytical parameters such as large linear dynamic range (LDR; 0.15–1.35 mM) of melamine detection, high sensitivity (80.6 μA mM−1 cm−2), low limit of detection (LOD; 0.118±0.005 mM), low limit of quantification (LOQ; 0.393 mM), and fast response time (30 s). Besides this, the good reproducibility (in several hours) and repeatability were investigated under identical conditions. Moreover, it was implemented to measure the long‐time stability, electron mobility, less charge‐transfer resistance, and analyzed diffusion‐controlled process for the oxidation reaction of the NPs assembled working GCE electrode, which showed outstanding chemical sensor performances. For validation, real environmental samples were collected from various water sources and investigated successfully with regard to the reliability of the selective melamine detection with prepared NPs coated sensor probe. Therefore, this approach might be introduced as an alternative route in the sensor technology to detect selectively unsafe chemicals by an electrochemical method with nanostructure‐doped materials for the safety of environmental, ecological, healthcare fields in a broad scale.