Zeolites are important materials for research and industrial applications. Mesopores are often introduced by desilication but other properties are also affected, making its optimization difficult. In this work, we demonstrate that Perturbation Theory and Machine Learning can be combined in a PTML multioutput model describing the effects of desilication. The PTML model achieves a notable accuracy ( R2 = 0.98) in the external validation and can be useful for the rational design of novel materials.