We have investigated the nature and extent of nanoscale disorder in prototypical host-guest zeolites, made of silicalite-1 (host) and organic structure directing agent (OSDA, guest). The four different selected OSDA-silicalite-1 differ in: the mineralizing agent used (Fvs. OH -), the synthesis' method (hydrothermal vs. solvent-free) and the OSDA (tetrapropylammonium TPA vs. tripropylethylammonium TPEA). The comparison between TPA and TPEA, chemically similar but differing in their symmetry, is examined in great detail owing to the novel relationship found between the geometrical disorder and the monoclinic-orthorhombic (m-o) phase transition occurring at low temperature. Long-and short-range organization and ordering are characterized by complementary XRD, Raman and multinuclear NMR ( 13 C, 14 N, 29 Si). The possibility of the m-o transition is studied by all these techniques at variable low T. An in-depth study of the disorder is carried out by x-ray structure determination and 2D NMR 29 Si-29 Si INADEQUATE correlations, including an up-to-date analysis of anisotropic atomic displacement parameters and a new fitting approach to estimate correlated disorder from 2D NMR datasets. The collected results allow to demonstrate how the disorder created by the positioning of the less symmetric TPEA guest leads to a correlated geometrical disorder for half of the atom sites in the host framework that completely inhibits the m-o phase transition.