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Abstract Here, we performed a systematic DFT study assisted by the workflow framework SimStack for the mechanical and thermodynamic properties of the clay mineral lizardite in pristine and six different types of O vacancies configurations. In most cases, the defect caused a structural phase transition in the lizardite from the trigonal (pristine) to the triclinic phase. The results show that oxygen vacancies in lizardite significantly reduce the lattice thermal conductivity, accompanied by an elastic moduli reduction and an anisotropy index increase. Through the P–V relation, an increase in compressibility was evidenced for vacancy configurations. Except for the vacancy with the same crystalline structure as pristine lizardite, the sound velocities of the other vacancy configurations produce a decrease in these velocities, and it is essential to highlight high values for the Grüneisen parameter. We emphasize the great relevance of the punctual-defects introduction, such as O vacancies, in lizardite, since this microstructural design is responsible for the decrease of the lattice thermal conductivity in comparison with the pristine system by decreasing the heat transfer ability, turning lizardite into a promising candidate for thermoelectric materials