Microfluidic paper-based assays represent a new approach to address the need for simple and cost-effective medical diagnostics. In an effort to couple paper-based assays with a similarly simple signal transduction, here we explored the feasibility of using potentiometric detection as a new modality to quantify affinity assays performed on a paper platform. As proof of principle a dot-blot model assay based on using IgE aptamer-gold nanoparticle conjugates was developed for the quantitative determination of IgE. The gold nanoparticle conjugates further catalyzed the deposition of silver nanoparticles that by oxidative dissolution generated silver ions. The silver ions were detected directly in the wet paper matrix by using a silver ion selective electrode. The analytical performance of potentiometric dot-blot assay matched that of reflectance-based assays, which suggests that potentiometric detection might represent a viable alternative to the conventionally used optical detection.