Primary carbonates in kimberlites are the main CO2 carriers in kimberlites and thus can be used to constrain the original carbon and oxygen-isotope composition of kimberlite melts and their deep mantle sources. However, the contribution of syn- and post-emplacement processes to the modification of the C–O-isotope composition of kimberlites is yet to be fully constrained. This study aims to shed new light on this topic through a detailed textural, compositional (major and trace elements), and in situ C–O–Sr isotopic characterisation of carbonates in the Benfontein kimberlite sills (Kimberley, South Africa). Our multi-technique approach not only reveals the petrographic and geochemical complexity of carbonates in kimberlites in unprecedented detail, but also allows identification of the processes that led to their formation, including: (1) magmatic crystallisation of Sr-rich calcite laths and groundmass; (2) crystallisation of late groundmass calcite from hydrothermal fluids; and (3) variable degrees of crustal contamination in carbonate-rich diapirs and secondary veins. These diapirs most likely resulted from a residual C–O–H fluid or carbonate melt with contributions from methane-rich fluids from the Dwyka shale wall rock, leading to higher 87Sr/86Sr and δ18O, but lower δ13C values than in pristine magmatic calcite. Before coalescing into the diapiric segregations, these fluids/melts also variably entrained early formed calcite laths and groundmass phases. Comparison between in situ and bulk-carbonate analyses confirms that O isotopic analyses of bulk carbonates from kimberlite rocks are not representative of the original isotopic signature of the kimberlite magma, whereas bulk C-isotope compositions are similar to those of the pristine magmatic carbonates. Calcite laths and most groundmass grains at Benfontein preserve isotopic values (δ18O = 6–8‰ and δ13C = − 4 to − 6‰), similar to those of unaltered carbonatites worldwide, which, therefore, probably correspond to those of their parental melts. This narrow range suggests kimberlite derivation from a mantle source with little contribution from recycled crustal material unless the recycled material had isotopic composition indistinguishable from typical mantle values.