Carbonates in fresh hypabyssal kimberlites worldwide have been studied to understand their origin i.e. primary magmatic (high T) versus deuteric (‘low T’) versus hydrothermal/alteration (‘low T’)] and identify optimal strategies for petrogenetic studies of kimberlitic carbonates. The approach presented here integrates detailed textural characterisation, cathodoluminescence (CL) imaging, in situ major- and trace-element analysis, as well as in situ Sr-isotope analysis. The results reveal a wide textural diversity. Calcite occurs as fine-grained groundmass, larger laths, segregations, veins or as a late crystallising phase, replacing olivine or early carbonates. Different generations of carbonates commonly coexist in the same kimberlite, each one defined by a characteristic texture, CL response and composition (e.g., variable Sr and Ba concentrations). In situ Sr isotope analysis revealed a magmatic signature for most of the carbonates, based on comparable ⁸⁷Sr/⁸⁶Sr values between these carbonates and the coexisting perovskite, a robust magmatic phase. However, this study also shows that in situ Sr isotope analysis not always allow distinction between primary (i.e., magmatic) and texturally secondary carbonates within the same sample. Carbonates with a clear secondary origin (e.g., late-stage veins) occasionally show the same moderately depleted ⁸⁷Sr/⁸⁶Sr ratios of primary carbonates and coexisting perovskite (e.g., calcite laths-shaped crystals with ⁸⁷Sr/⁸⁶Sr values identical within uncertainty to those of vein calcite in the De Beers kimberlite). This complexity emphasises the necessity of integrating detailed petrography, geochemical and in situ Sr isotopic analyses for an accurate interpretation of carbonate petrogenesis in kimberlites. Therefore, the complex petrogenesis of carbonates demonstrated here not only highlights the compositional variability of kimberlites, but also raises concerns about the use of bulk-carbonate C-O isotope studies to characterise the parental melt compositions. Conversely, our integrated textural and in situ study successfully identifies the most appropriate (i.e. primary) carbonates for providing constraints on the isotopic parameters of parental kimberlite magmas.