Surface-enhanced Raman scattering (SERS) is observed solitarily for analytes that are placed in the vicinity of plasmonic nanoparticles since the amplitude of the electric field on their surface decays with distance. Taking this idea forward, we have designed core-shell plasmonic systems for SERS sensing, consisting of silver nanoparticles coated with mesoporous silica (Ag@m-SiO2) having an average pore size of 2.4 nm. Studies presented herein show that a Ag nanoparticle core of similar to 55 nm and an m-SiO2 shell of similar to 40 nm represent a preferred combination for sieving and sensing, established by following the SERS of a standard marker, namely, rhodamine 6G. However, under identical conditions, Ag nanoparticles capped with microporous silica (Ag@SiO2) inhibit the passage of analyte molecules into the plasmonic field. Yet another level of selectivity is provided by the negative surface charge of Ag@m-SiO2 (zeta = -33 mV), eliminating negatively charged molecules from SERS sensing due to strong electrostatic repulsion. These aspects are confirmed using pyrene molecules, which are neutral, and pyrene derivatives carrying positive and negative charges. Thus, the SERS signal arises only from the neutral and positively charged molecules, which can penetrate into the pores, and not from the negatively charged analytes. The practical application of Ag@m-SiO2 having a shell thickness of similar to 40 nm for SERS sensing has been established using two commonly used organophosphorus pesticides (quinalphos and triazophos) directly from various vegetable matrices after the removal of plant pigments. The mesoporous silica shell of Ag@m-SiO2 having a thickness of similar to 40 nm sieves large molecules such as proteins and keeps them away from the electric field generated by the Ag nanoparticle, thus enabling the sensing of small molecules such as pesticides that penetrate into the shell.