Carbonatites are relatively rare rocks with only about 600 occurrences world-wide. While dominated by intrusive carbonatites the rock record only shows about 50 occurrences of extrusive carbonatites. The geochemical link between intrusive and extrusive equivalents is essentially unstudied. To shed light on this topic the interface between fine-grained dolomite-carbonatite dykes and associated diatremes of the Gross Brukkaros in central Namibia was investigated. Whole rock geochemistry and petrography provide evidence that the carbonatite dykes contain significant amounts of Si and Al, which is assigned to assimilation of crustal xenoliths. At the transition from carbonatite dyke to diatreme formation, the carbonatite melt degassed (release of CO2 and other volatiles to the atmosphere), while the Si, Ca, Mg and Fe load together with a high amount of trace elements became precipitated from a hydrothermal “magmatic-provenance-dominated” fluid during rapid temperature drop in the course of decompression as a mixture of micro- and cryptocrystalline quartz (quartz I) and aegirine-augite (plus minor magnetite). This mineral assemblage forms the matrix of the diatreme breccia. A second quartz generation (quartz II) is formed in the post-eruption environment by precipitation from a fluid resulted by a mixture of remaining fluids and an influx of meteoric waters. All measured trace elements show significantly higher contents in quartz I compared to quartz II (with exception of Li). This study provides the first holistic dataset that show how a carbonatite geochemically behave during eruption.