The isotopes of carbon (δ13C) and oxygen (δ18O) in ancient soil (paleosol) carbonates have been used for nearly a half century to reconstruct terrestrial paleoenvironmental change in eastern Africa. These measurements have resolved the late Miocene expansion of grasslands - in Africa and worldwide - and Plio-Pleistocene aridification, respectively. In the last decade, a third stable isotope measurement, carbonate clumped isotopes, has been applied alongside δ13C and δ18O to great effect. In tropical settings with low seasonality, soil carbonate clumped isotope paleothermometry seems to faithfully record mean annual temperature, however, like δ13C and δ18O, clumped isotopes are sensitive to secondary and non-pedogenic carbonate mineralization. We demonstrate, using new records from the late and early Miocene in the Turkana Basin, that while primary pedogenic carbonate textures seem to retain paleotemperature and isotopic information, they are susceptible to overprinting in burial settings. These diagenetic effects must be considered, and dealt with or avoided altogether, to reconstruct continental paleoclimate and paleoenvironment during this time.