We utilize carbonate clumped isotope thermometry to explore the diagenetic and thermal histories of exhumed brachiopods, crinoids, cements, and host rock in the Permian Palmarito Formation, Venezuela, and the Carboniferous Bird Spring Formation, Nevada, USA. Carbonate components in the Palmarito Formation, buried to ∼4 km depth, yield statistically indistinguishable clumped isotope temperatures [T(Δ47)] ranging from 86 to 122 °C. Clumped isotope temperatures of components in the more deeply buried Bird Spring Formation (>5 km) range from ∼100 to 165 °C and differ by component type, with brachiopods and pore-filling cements yielding the highest T(Δ47) (mean = 153 and 141 °C, respectively) and crinoids and host rock yielding significantly cooler T(Δ47) (mean = 103 and 114 °C). New high-resolution thermal histories are coupled with kinetic models to predict the extent of solid-state C-O bond reordering during burial and exhumation for both sites. Application of these models, termed “THRMs” (thermal history reordering models), suggests that brachiopods in the Palmarito Formation experienced partial bond reordering without complete equilibration of clumped isotopes at maximum burial temperature. In contrast, clumped isotope bonds of brachiopods from the Bird Spring Formation completely equilibrated at maximum burial temperature, and now reflect blocking temperatures achieved during cooling. The 40–50-°C-cooler clumped isotope temperatures measured in Bird Spring Formation crinoids and host rock can be explained by recrystallization and cementation during shallow burial combined with a greater inherent resistance to solid-state reordering than brachiopods.