Coke formation during the isobutane/butene alkylation reaction over zeolites decreases the acidity and acid strength of the catalysts. Microcalorimetric measurements of the differential heat of pyridine adsorption and FTIR spectroscopy of adsorbed pyridine were used to probe the changes in the acid properties caused by the deactivation processes. Specifically, fresh and deactivated commercial acid catalysts such as REY, USY, and Beta zeolite were studied. The adsorption microcalorimetry and FTIR spectroscopy results demonstrated that USY has the strongest acid sites (both Bronsted and Lewis) and the highest concentration of strong sites followed by REY and then by Beta zeolite. This order is the opposite of that observed for the alkylation catalytic performance of these zeolites. In particular, it seems that having a high concentration of strong Lewis sites promotes catalyst deactivation. The deposits formed during deactivation have a strong paraffinic character, but evidence of olefinic species is also observed. The degree of unsaturation of the surface species formed increases from Beta to USY zeolite, implying that the presence of a high concentration of strong Lewis-acid sites promotes the formation of unsaturated compounds. Bronsted sites with intermediate acid strength appear to be the appropriate sites for maintaining good alkylation catalytic performance. The best catalytic performance and the slowest deactivation were achieved with Beta zeolite, followed by REY and USY with low sodium content. Only butene isomerization was observed for USY with high sodium content. For the active catalysts, the alkylation global reaction route dominates initially, but the amount of alkylation products decreases as the catalyst starts deactivating when oligomerization predominates; and, finally, the catalyst loses most of its activity and isomerization is the only reaction observed. The product distribution obtained suggests that, instead of authentic alkylation, the initial prevalent mechanism is polymerization followed by beta-scission. Two deactivation models are proposed to explain the deactivation. The direct obstruction of the alkylation active sites by irreversible adsorption of coke or coke precursors and the indirect obstruction of the active sites by pore blocking or pore filling.