The development of a high-performance electrochemical sensing platform for monitoring nitrofurantoin (NFT) levels in various real samples plays an important role in the research community worldwide. To accomplish this objective, the crucial challenge is to construct sensing interfaces with outstanding electrocatalytic capabilities. In the present work, a highly efficient metal@carbon electrocatalyst with porous and multi-core–shell nanobox structure comprising polydopamine (PDA)-derived C coated NiCo@C and FeCo@C nanohybrid (named as NiCo@C/FeCo@C@C) was fabricated by simply pyrolyzing NiCo@FeCo Prussian blue analogues (PBA)@PDA. The carbonization of PDA into carbon shells protected the framework from collapsing during high-temperature pyrolysis process, thus enlarging the specific surface areas and porosity. The NiCo@C/FeCo@C@C composite attained an enhanced electrochemical capability, such as an outstanding electronic conductivity from the double carbon shell with porous structure, a large number of active sites and a high electrocatalytic activity from the metallic alloy nanoparticles, which exhibited a highly sensitive response to NFT. Under optimized experimental conditions, the established NiCo@C/FeCo@C@C electrochemical sensor displayed a wide linear range of 0.05–100 μM for NFT determination, coupled with a low detection limit of 14 nM. The practical feasibility of this sensor was also confirmed by the analysis of NFT in tablet and lake water samples with outstanding recovery rates. Moreover, the sustainability of the sensor was demonstrated through its prominent performance in high reproducibility, selectivity and long-term stability. This study thus introduces an innovative approach for the advance of highly efficient electrocatalysts in the area of electrochemical sensing.