Mineral chemistry, textures and geochemistry of syenite autoliths from Kilombe volcano indicate that they crystallized in the upper parts of a magma chamber from peralkaline trachytic magmas that compositionally straddle the alkali feldspar join in the “residuum system” (ne = 0–1.03; qz = 0–0.77). Mineral reaction and/or overgrowth processes were responsible for the replacement of (i) Mg–hedenbergite by aegirine–augite, Ca–aegirine and/or aegirine, (ii) fayalite by amphiboles, and (iii) magnetite by aenigmatite. Ti–magnetite in silica-saturated syenites generally shows ilmenite exsolution, partly promoted by circulating fluids. By contrast, the Fe–Ti oxides in the silica-undersaturated (sodalite-bearing) syenites show no signs of deuteric alteration. These syenites were ejected shortly after completion of crystallization. Ilmenite–magnetite equilibria indicate fO2 between − 19.5 and − 23.1 log units (T 679–578 °C), slightly below the FMQ buffer. The subsequent crystallization of aenigmatite and Na-rich pyroxenes suggests an increase in the oxidation state of the late-magmatic liquids and implies the influence of post-magmatic fluids. Irrespective of silica saturation, the syenites can be divided into (1) “normal” syenites, characterized by Ce/Ce ratios between 0.83 and 0.99 and (2) Ce-anomalous syenites, showing distinct negative Ce-anomalies (Ce/Ce 0.77–0.24). “Normal” silica-saturated syenites evolved towards pantelleritic trachyte. The Ce-anomalous syenites are relatively depleted in Zr, Hf, Th, Nb and Ta but, with the exception of Ce, are significantly enriched in REE. The silica-saturated syenites contain REE–fluorcarbonates (synchysite-bastnaesite series) with negative Ce-anomalies (Ce/Ce 0.4–0.8, mean 0.6), corroded monazite group minerals with LREE-rich patches, and hydrated, Fe- and P-rich phyllosilicates. Each of these is inferred to be of non-magmatic origin. Fractures in feldspars and pyroxenes contain Pb-, REE- and Mn-rich cryptocrystalline or amorphous material. The monazite minerals are characterized by the most prominent negative Ce-anomalies (Ce/Cemean = 0.5), and in the most altered and Ca-rich areas (depleted in REE), Ce/Ce is less than 0.2. It is inferred that carbonatitic fluids rich in F, Na and lanthanides but depleted in Ce by fractional crystallization of cerian pyrochlore, percolated into the subvolcanic system and interacted with the syenites at the thermal boundary layers of the magma chamber, during and shortly after their crystallization. Chevkinite–(Ce), pyrochlore, monazite and synchysite-bastnaesite, occurring as accessory minerals, have been found for the first time at Kilombe together with eudialyte, nacareniobsite–(Ce) and thorite. These latter represent new mineral occurrences in Kenya.