Since the catalytic activity and the stability of silica-bound organometallic complexes are affected by their interactions with hydroxyl groups on the surface, isolated hydroxyls are often created prior to the introduction of catalytic species. Here, we investigate a method to remove the indigenous hydroxyls and create new isolated hydroxyls by grafting organo-trimethoxysilane (R-TMS) to generate a silicon T2 site, (≡SiO‒)2SiR(‒OH). We used in situ 29Si solid-state NMR experiments to monitor the evolution of Tn sites, (≡SiO‒)nSiR(‒OH)3-n (n = 1, 2, 3). The study indicates that i) the grafting proceeds in a consecutive manner as T1 → T2 → T3, and ii) the kinetics depend on the type of functional groups in the silane. However, the rates of T1 formation and T2 → T3 conversion are also controlled to a significant extent by the entropy loss associated to the initial silane binding and the spatial arrangement of surface hydroxyls, respectively. The grafting of R-TMS with a basic functional group leads to a lower concentration of T1 sites. The nucleophilicity of the functional group facilitates the grafting process by lowering the enthalpy barrier, while the T1 formation rate is more influenced by the entropy barrier than the T1 → T2 conversion rate. Thus, the basic functional group promotes the T1 → T2 conversion more than the T1 formation, resulting in a lower concentration of T1 sites.