We describe an approach to estimating the crystallization temperatures of diagenetic calcites using clumped-isotope thermometry, a paleothermometer based on the 13C–18O-bond enrichment in carbonates. Application of this thermometer to calcified gastropod shells and calcite cements in an early Eocene limestone from the Colorado Plateau reveals a record of calcite precipitation and replacement at temperatures varying from 14 to 123°C. The early Eocene host sediments were never deeply buried, but they experienced a significant thermal pulse associated with the emplacement of a late Miocene basalt flow. The combination of independent constraints on thermal history with clumped-isotope thermometry, petrographic (including cathodoluminescence) observations, and oxygen isotopic data provides an improved basis for estimation of the temperature and timing of diagenetic events and fluid sources. The petrography and calcite δ18O values, taken alone, suggest that the aragonite-to-calcite transformation of gastropod shell material occurred simultaneously with early formation of cements and lithification of the matrix in the same sample. However, addition of clumped-isotope thermometry demonstrates that this phase transformation of shell material occurred at temperatures of 94–123°C in a highly rock-buffered microenvironment (i.e., with the isotopic composition of fluid buffered by coexisting carbonate), millions of years after lithification of the matrix and formation of initial low-temperature (14–19°C) calcite cements within shell body cavities. Clumped-isotope temperatures in excess of reasonable Earth-surface conditions recorded by later-formed cements demand that cement growth occurred in association with the lava emplacement. Our results illustrate the potential for clumped-isotope thermometry to constrain conditions of diagenesis and guide interpretations that would not be possible on the basis of conventional stable-isotopic and petrographic data alone, and demonstrate how petrographic characterization of clumped-isotope thermometry samples can benefit paleoclimate studies.