The Basal Complex of Fuerteventura, in the Canary Islands, contains an ultra-alkaline complex formed by alkaline pyroxenites, melteigites, ijolites, alkaline gabbros, syenites and carbonatite dykes cut by a basaltic dyke swarm. A later basaltic magma, which formed a pyroxenite-gabbro pluton, intruded the entire series and caused a strong contact metamorphism and partial melting of the rocks near the contact. The anatexis appears in the form of “zebra rocks” in the contact-metamorphosed silicate rocks. Carbonatite dykes have been found in the metamorphic aureole and in the anatexite. Typical skarn mineralogy, including diopside, grossular-andradite garnet and vesuvianite, developed between the carbonatites and silicate rocks (e.g. ijolites, pyroxenites). In the metacarbonatites and skarns, the metamorphic paragenesis varies with the distance to the contact zone. The original igneous mineralogy disappeared completely in the anatectic zone, and a metamorphic association composed of wollastonite, monticellite, diopside, vesuvianite, garnet, calcite, perovskite, alabandite, pyrrhotite and Nb–Zr–Ca silicates (cuspidine–niocalite–baghdadite series) was formed. This paragenesis indicates that the carbonatites within the anatectic zone have undergone a thermal metamorphism under hornblende–hornfels facies (550–600°C). Metamorphic reactions were also associated with the infiltration of F-rich aqueous fluids, which produced an intense metasomatism and caused Sr, Ba and S enrichment in the carbonatite. As a result, alkali elements such as K, Na, Rb or Th were leached and the remaining chemical elements were redistributed into the neoformed metacarbonatite paragenesis.Most of the metacarbonatites show significant C and O isotope deviations as compared with the primary isotopic compositions, due to fluid/rock interactions. The metacarbonatites with wollastonite have δ13C and δ18O values indicating CO2 release, in agreement with devolatilization reactions that took place in the metacarbonatite and in the skarn. In addition, in the metacarbonatites with diopside, vesuvianite and garnet, a δ18O decrease relative to the primary isotopic compositions due to late fluid/rock interactions can be observed. The circulation of hot meteoric water fluids heated by the pyroxenite intrusion was responsible for the metamorphic-metasomatic reactions that caused the mineralogical, chemical and isotopic changes in the carbonatitic rocks and brought about skarn formation.