Stable isotope data from the Jurassic Qaqarssuk Carbonatite Complex show that carbonatites intruded during the main intrusive event have δ18O-values ranging from +7 to +8.1‰ SMOW and δ13C-values ranging from −3.5 to −3.1‰ PDB.Late-stage søvite veins are enriched in light carbon relative to the main-stage carbonatites, with δ13C-values ranging from −5 to −4‰ PDB. This is interpreted as loss of heavy carbon to a gas phase.Late-stage REE-carbonatites have δ3C-values in the same range as the main-stage carbonatites, but elevated δ3C-values relative to late-stage søvites. The REE-carbonatites have elevated δ18O-values (+7.4 to +9.2‰ SMOW) relative to both main-stage carbonatites and late-stage søvite.Carbonates in metasomatically altered basement and contaminated carbonatite have elevated δ18O-values (+8.2 to +8.8‰ SMOW), probably caused by exchange of oxygen with the basement.Oxygen isotope geothermometry give temperatures in the range 313–608°C, which is low relative to the expected igneous temperatures. These low temperatures are explained as caused by subsolidus reactions such as exsolution and recrystallization which can be observed in the carbonates. There is poor correspondence between oxygen and carbon isotope geothermometry as well as with solvus geothermometry, indicating that the calibration of the isotope geothermometer established in metamorphic carbonate rocks cannot be applied directly to carbonatites.