Zeolites are microporous aluminosilicate materials used as industrial catalysts, and there is much interest in understanding their catalytic behavior. The adsorption of methanol in the catalytically active zeolite chabazite and in sodalite was examined by performing ab initio calculations within periodic boundary conditions. A direct correlation between zeolite structure and chemical activation of the adsorbate was found. Methanol was protonated without an activation energy by a Brønsted acid site, provided the molecule was situated in the eight-ring window of chabazite, whereas the same molecule was only physisorbed in more open cage regions, such as those found in sodalite.