We demonstrate a methodology to prepare Au-core-Ag-shell nanoparticles displaying both SERS and surface-enhanced fluorescence (SEF) activities simultaneously by embedding dye molecules between the core and the shell. Polyelectrolytes are used to adjust the spacing and the dye position between the core and the shell. Layer-by-layer polyelectrolyte deposition can serve as an effective and flexible way to introduce various types of dye molecules into the nanostructures. Results from the spectral measurements shed light on the intricacy between SERS and SEF.