Songwe Hill, Malawi, is one of the least studied carbonatites but has now become particularly important as it hosts a relatively large rare earth deposit. The results of new mapping, petrography, geochemistry and geochronology indicate that the 0.8 km diameter Songwe Hill is distinct from the other Chilwa Alkaline Province carbonatites in that it intruded the side of the much larger (4 × 6 km) and slightly older (134.6 ± 4.4 Ma) Mauze nepheline syenite and then evolved through three different carbonatite compositions (C1–C3). Early C1 carbonatite is scarce and is composed of medium–coarse-grained calcite carbonatite containing zircons with a U–Pb age of 132.9 ± 6.7 Ma. It is similar to magmatic carbonatite in other carbonatite complexes at Chilwa Island and Tundulu in the Chilwa Alkaline Province and others worldwide. The fine-grained calcite carbonatite (C2) is the most abundant stage at Songwe Hill, followed by a more REE- and Sr-rich ferroan calcite carbonatite (C3). Both stages C2 and C3 display evidence of extensive (carbo)-hydrothermal overprinting that has produced apatite enriched in HREE (<2000 ppm Y) and, in C3, synchysite-(Ce). The final stages comprise HREE-rich apatite fluorite veins and Mn-Fe-rich veins. Widespread brecciation and incorporation of fenite into carbonatite, brittle fracturing, rounded clasts and a fenite carapace at the top of the hill indicate a shallow level of emplacement into the crust. This shallow intrusion level acted as a reservoir for multiple stages of carbonatite-derived fluid and HREE-enriched apatite mineralisation as well as LREE-enriched synchysite-(Ce). The close proximity and similar age of the large Mauze nepheline syenite suggests it may have acted as a heat source driving a hydrothermal system that has differentiated Songwe Hill from other Chilwa carbonatites.