Glycoside hydrolases (GHs) are enzymes that catalyze the hydrolysis of the glycosidic bond between two carbohydrate residues or a carbohydrate unit linked to a non-carbohydrate aglycon unit. Despite years of research dedicated to GHs, there are still several mechanistic details, relevant for individual GH enzymes, that remain to be investigated. In this work, a computational analysis of the detailed mechanism of several GHs is presented. QM/MM metadynamics simulations of two glycoside hydrolases, GH8 endoglucanase and GH43 β-xylosidase, give insight into the enzymatic deconstruction of the plant cell wall, and the detailed reaction mechanism of both enzymes. In addition, an investigation of the GH-imposed twisting of substrate glycosidic bonds in 14 different GH families is presented. Finally, a QM/MM metadynamics simulation of Golgi α-mannosidase unravels the hydrolysis mechanism of this enzyme, which is a target against breast, colon and skin cancer.