The microscopic behavior of the Ca-zeolite yugawaralite has been studied by ab initio molecular dynamics simulations adopting experimental cell parameters obtained at pressures up to ~9 GPa. Pressure-induced volume contraction occurs via rotations of quasi-rigid TO4 tetrahedra that reduce the size of the channels in which the extra-framework species are located. Such rotations are governed by deformation of the coordination polyhedron of Ca, which is made up of water and framework O atoms. Contraction of the Ca-H2O distances is favored at moderate pressure; at higher pressure the shortening of Ca-framework O atom distances becomes prevalent. The hydrogen bond network plays a fundamental role in the overall response to pressure. Our results indicate that the high-P-induced deformation of the framework structure is strictly correlated to the extra-framework species that act as “templates” in the compression process.