To address the issue of poor selectivity in nanotechnology-driven, portable nitroaromatics sensors, we have coupled a ratiometric fluorescence sensor based on silicon quantum dots and fluorescent proteins with a colorimetric, enzyme-based sensor. Together, the sensors allow differentiation of nitroaromatic compounds – specifically, distinguishing acetylcholinergic nerve agents from the explosive compounds explored herein. The combined system can detect 2,4,6-trinitrotoluene, 2,4- dinitrotoluene and 4-nitrophenol with micromolar detection limits and affords subsequent differentiation from the nitro-containing nerve agent paraoxon. This demonstrates the advantage of merging elements of materials chemistry and biochemistry to devise customized sensors which can accurately identify hazardous chemical species.