Risks associated with carbonation are a key limitation to greater replacement levels of ordinary portland cement (OPC) by supplementary cementitious materials (SCMs). The addition of pozzolanic SCMs in OPC alters the hydrate assemblage by forming phases like calcium-(alumina)-silicate-hydrate (C-(A)-S-H). The objective of the present study was to elucidate how such changes in hydrate assemblage influence the chemical mechanisms of carbonation in a realistic OPC system. Here, we show that synthetic zeolite Y (faujasite) is a highly reactive pozzolan in OPC that reduces the calcium content of hydration products via prompt consumption of calcium hydroxide from the evolving phase assemblage prior to CO2 exposure. Suppression of portlandite at moderate to high zeolite Y content led to a more damaging mechanism of carbonation by disrupting the formation of a passivating carbonate layer. Without this layer, carbonation depth and CO2 uptake are increased. Binders containing 12–18% zeolite Y by volume consumed all the calcium hydroxide from OPC during hydration and reduced the Ca/(Si+Al) ratio of the amorphous products to near 0.67. In these cases, higher carbonation depths were observed after exposure to ambient air with decalcification of C-(A)-S-H as the main source of CO2 buffering. Binders with either 0% or 4% zeolite Y contained calcium hydroxide in the hydrated microstructure, had higher Ca/(Si+Al) ratios, and formed a calcite-rich passivation layer that halted deep carbonation. Although the carbonated layer in the samples with 12% and 18% zeolite Y contained 70% and 76% less calcite than the OPC respectively, their higher carbonation depths resulted in total CO2 uptakes that were 12x greater than the OPC sample. Passivation layer formation in samples with calcium hydroxide explains this finding and was further supported by thermodynamic modeling. High Si/Al zeolite additives to OPC should be balanced with the calcium content for optimal carbonation resistance.