We have used sol-gel methods to immobilize gold-silica nanoshells to create robust SERS based sensors. Using a protocol commonly used to immobilize proteins, biologically friendly SERS sensors for the study of gold binding peptides and proteins have been created. Specifically, by combining tetramethyl orthosilicate (TMOS), methyltrimethoxysilicate (MTMS), phosphate buffer, and gold nanoparticles we have created sol-gels with reduced fluorescence and Raman backgrounds. The resulting substrates have been tested using the Raman scattering response of 4-mercaptonbenzoic acid (4-MBA) to determine porosity and long-term stability of this SERS substrate. Multiple rinse cycles using phosphate buffer showed no significant decline in the SERS response of the substrate up to ten rinse cycles. Future studies will test the feasibility of using such substrates for the detection of biomolecules on the surface of gold.