Metal-organic frameworks (MOFs) are crystalline materials with novel physical and chemical properties. Computational simulations have become powerful complements to experiment for understanding catalysis in MOFs and developing new MOFs and their applications. However, due to their relatively large and complex structures, MOFs can be burdensome for fully quantum mechanical calculations. A combined quantum mechanical and molecular mechanical (QM/MM) method that combines the accuracy of fully quantum mechanical methods and the efficiency of MM methods is therefore attractive. In this study, we employ a QM/MM method for the study of two classes of chemical process in a MOF: the conversion of reaction intermediates in an Ir-containing borylation catalyst supported on MOF UiO-67 and the diffusion of a diborylated methane molecule in the pristine UiO-67 framework. We compare the QM/MM results with full-quantum mechanical results on large systems to validate the accuracy of the applied QM/MM method. In the first case, we consider a model of the entire system by partitioning it into subsystems that interact covalently, and in the second case the subsystem interaction is mainly steric. We observe that the QM/MM results agree with the full-quantum mechanical results within an average of 4 kcal/mol in the first case with strong electronic interactions and within an average of 3 kcal/mol in the case with only noncovalent interactions. An important lesson learned from the present study is that the quantitative results are very sensitive to the lattice constants predicted by the MM method used in the QM/MM calculations.