Abstract Carbonate clumped isotope thermometry (T( Δ 47 )) and the oxygen stable isotope record ( δ 18 O ) provide critical constraints on the temperature of carbonate mineral formation and isotopic composition of ancient waters used in reconstructions of past climate, tectonics, and ecological and environmental change. The robust use of these proxies requires that carbonate minerals in the rock record retain primary isotopic compositions through often complex post-depositional thermal histories. New carbonate clumped isotope thermometry and sedimentology data are paired with existing thermochronology and isotope exchange reaction modeling to provide unique constraints on the alteration history of the carbon and oxygen isotopes in Tethyan marine carbonates (Jialazi Fm, Tso Jianding Group) of the Xigaze forearc, southern Tibet. Within the framework of the textural and isotopic data, the effects of early and late burial alteration on Δ 47 and δ 18 O values of marine rocks that were buried to 4 km above sea level are modeled. The alteration products are considered within two well-studied mechanistic frameworks: water-rock recrystallization and solid-state reordering of 13 C 18 O bonds at high temperature. The proposed alteration model is as follows: (1) shallow, early diagenesis with water of similar composition and temperature to formation waters infills primary porespace with microspar; (2) high-temperature, rock-buffered water-rock exchange and partial solid-state reordering at >3–4 km depth; and (3) near-surface, low-temperature water-rock exchange on the exhumation pathway. The Δ 47 heterogeneity within individual samples (0.456 to 0.721) requires significant differential alteration on the retrograde path (high to low temperature, low water-rock ratio) in which primary compositions and compositions inherited during early burial diagenesis are overprinted with modern meteoric values. A low T( Δ 47 ) value is often assumed to record the primary temperature of the depositional environment. However, samples yielding low T( Δ 47 ) values in the Jialazi Fm have undergone extensive high-temperature water-rock alteration, and therefore, require a mechanism for increasing 13 C 18 O bond ordering on the retrograde pathway while preserving many primary biogenic structures and micritic textures. This study highlights the potential significance of late-stage, low-temperature alteration of carbonates derived from orogenic sedimentary basins for studies of terrestrial paleoenvironments and tectonics. This study also provides an example framework for combining observational and analytical data to reconstruct a carbonate alteration history of a buried sedimentary package.