The coating of gold nanorods with a silica shell (AuNR@SiO2) is an effective way to extend their use in a wide variety of biomedical applications. A silica shell offers numerous advantages as it provides more stability, frees the surface from toxic cetyltrimethylammonium bromide (CTAB), and preserves the rod shape under photothermal conditions. We introduce herein a new strategy to perform this coating based on dissociation of tetraethylorthosilicate (TEOS) hydrolysis and condensation reactions. This dissociation is achieved by a pH modulation of the reaction medium, and, depending on selected pH conditions, AuNR@SiO2 with thick silica shell having an organized mesoporosity aligned either parallel (AuNR@//m-SiO2) or perpendicular (AuNR@⊥m-SiO2) to the AuNR surface were generated. Moreover, when mercaptopropyltrimethoxysilane (MPTMS) was used as a surface primer prior to TEOS condensation, ultrathin and homogeneous silica shells (AuNR@t-SiO2) of controllable thickness in the range 2-6 nm, are produced. These protocols proved robust enough to prevent contamination with core-free silica particles. While formation, at high TEOS concentration of these nanoparticles, is evidenced by TEM analysis before the purification procedure, their total elimination during the purification step was achieved by addition of a suitable amount of CTAB to ensure the colloidal stability of the core-free and core-shell nanoparticles. Complete elimination of CTAB was demonstrated by SERS when ligand exchange of CTAB by MPTMS is first carried out. In a preliminary study, AuNR@t-SiO2 particles were used to build up a nanoprobe aimed at the label-free plasmonic immunodetection of a model target in solution.