Metal active sites exchanged in zeolites dynamically change speciation under different reaction conditions, resulting in condition-dependent reactivity with gas molecules. This is of particular significance in chemical deactivation, such as sulfur poisoning of Cu-SSZ-13 zeolites used for NH3-assisted selective catalytic reduction (SCR) of NOx in diesel engine exhaust. Here, we employ computational techniques, combined with experiments and spectroscopies, to develop thermodynamic models for sulfur poisoning of zeolite framework-bound Cu dimers that form at high temperatures in Cu-SSZ-13 zeolites as a function of both the Al distribution and reaction conditions. Our results demonstrate that framework-bound Cu dimers that form under high temperature oxidative conditions are particularly susceptible to poisoning by SO2 and SO3. These Cu dimers react more exothermically with SOx species than Cu monomers, forming thermodynamically stable sulfur-containing Cu dimers that require high temperatures for catalyst regeneration.