Clathrate hydrates are crystalline materials made of water molecules forming host cages within which guest molecules are located. The hydrogen bond network ensuring the stability of the host substructure includes ionic defects, having an impact on the physicochemical properties of the systems. In this paper, a new way of introducing these ionic defects is proposed. Type II clathrate hydrates mixing tetrahydrofuran (THF) and perchloric acid guest molecules are synthesized and investigated by means of calorimetric, X-ray diffraction, and Raman scattering measurements together with a computational structure relaxation in the density functional theory approximation. The formation of the mixed clathrate hydrate with perchlorate anion included in the large cage of the cationic host-substructure of the THF type II clathrate hydrate requires the cooling of a (1-α) THF·αHClO4·17H2O solution with α less than 0.125. Above this inherent limitation, a multiphasic regime is observed in the formation of clathrate hydrate (mixture of type I and type II). The substitution of a THF molecule per perchlorate anion allows the modification of the melting of the type II clathrate hydrate, by preserving the clathrate structure. Shrinkage of the type II unit cell is measured together with a softening of the host lattice mode. In the harmonic approximation, the observation of both phenomena is counterintuitive and outline existing competition between anharmonicity of the cage energy landscape and ionic host–guest interaction. This study reveals the key role played by acidic defects existing in the host substructure on the physicochemical properties of clathrate hydrate.