Surfaced enhanced Raman scattering (SERS) has been extensively exploited for label-free and non-destructive biochemical detections. Recently diverse SERS substrates have been reported to improve sensitivity of SERS. However, the current platforms still have technical limitation for in vivo applications. Here, we report a nanoplasmonic biopatch of plasmonic nanoparticles physically embedded in highly biocompatible and Raman inactive agarose hydrogel. Molecular diffusion of small molecules such as neurotransmitter through nanoplasmonic biopatch was quantitatively visualized without labeling by using real-time microscopic SERS. In particular, the nano/micro porous structures within agarose hydrogel allow the SERS detection of macromolecules such as amyloid fibrils. This soft SERS platform opens up new opportunities for in vivo SERS applications.