Assays for biointeractions of molecules with supported lipid bilayers using fluorescence superquenching are described. A conjugated cationic polymer was adsorbed on to silica microspheres, which were then coated with an anionic lipid bilayer. The lipid bilayer attenuated superquenching by acting as a barrier between the conjugated polymer and its quencher. Biointeractions of the lipid bilayer with a membrane lytic peptide, melittin, were detected and quantitated by superquenching of the conjugated polyelectrolyte in flow cytometric and microfluidic bioassays. A higher sensitivity for detecting melittin lysis of the lipid bilayer at lower concentrations and shorter times for melittin action was found using flow cytometry in this study in comparison to other existing methods. This study combined the sensitivity of superquenching and flow cytometry to detect biointeractions with a lipid bilayer, which serves as a platform for developing functional assays for sensor applications, lipid enzymology, and investigations of molecular interactions. In addition, this study demonstrated proof-of-concept for using superquenching detected as a result of lipid bilayer disruption in a rnicrofluidic format.