Molecular simulation, through the computation of adsorption isotherms, is a useful predictive tool for the selective capacity of nanoporous materials. Generally, adsorbents are modelled as rigid frameworks, as opposed to allowing for vibrations of the lattice, and this approximation is assumed to have negligible impact on adsorption. In this work, this approach was tested in an especially challenging system by computing the adsorption of the chiral molecules 2-pentanol, 2-methylbutanol and 3-methyl-2-butanol in the all-silica and germanosilicate chiral zeolites STW and studying their lattice vibrations upon adsorption. The analysis of single- and multicomponent adsorption isotherms showed the suitability of STW-type zeolites as molecular sieves for chiral separation processes, which pose a challenging task in the chemical and pharmaceutical industries. Moreover, new experimental adsorption data validate the force field employed. The results reveal that the lattice vibrations of the all-silica framework are sorbate-independent, while those of germanosilicate STW show host–guest coupling modulated by uptake and sorbate type that disrupts the chiral recognition sites. This study indicates that the effects of intrinsic flexibility on the selective capacity of nanoporous materials may range from low to high impact, and some of them could not have been foreseen even after examination of the structural dynamics of an empty framework.