Surface-enhanced Raman scattering (SERS) induced by metal nanoparticles (NPs) or nanostructures is a key to overcoming the low Raman signal. However, metal surface being vulnerable to contamination by protein makes it challenging to detect only target molecules in a complex medium. Herein, we design plasmonic microgels through simultaneous photoreduction and photocross-linking. Water-in-oil (W/O) emulsions are produced using microfluidics. Emulsions are irradiated to form hydrogel network and gold nanoparticles. Here, hydrogel network serves as a filter to exclude protein, which is larger than the pore size of PEGDA mesh. Under the heat, unreacted gold precursor is reduced by sodium citrate, leading to the formation of new gold NPs or the growth of pre-formed gold NPs. Concentration of sodium citrate is optimized for SERS sensitivity and microgels show SERS signal uniformity. As a proof of concept, we successfully detected a biomarker of sepsis called pyocyanin from saliva.