To detect chemical or biological threats, it is crucial that sensor devices can differentiate various target molecules. In general, each different sensing method has its own strengths and weaknesses due to their respective limitations. For example, although resonant sensors have high sensitivity, they are not able to discriminate target molecules. At the same time, although surface-enhanced Raman spectroscopy is a representative label-free detection method that can discriminate target molecules, its fabrication is often complex and expensive. Here we present a label-free multimodal nanoporous resonator-based system for small molecule detection and discrimination that combines the strengths of each of these sensing methods. Our approach is not only able to improve the sensitivity of the resonant sensor but it can also discriminate the target molecules. Furthermore, the fabrication process is swift (lasting <3 min) and convenient.