A combined optical and electron microscopy (SEM, EDS, and EPMA) study was conducted on ten rock samples from the Proterozoic San José del Guaviare Syenite (SJGS), southeastern Colombia, to utilize minor and trace minerals in interpreting the magmatic evolution of these silica undersaturated rocks. The major minerals of the sampled syenites are nepheline, Fe-rich clinopyroxene, amphibole, alkali feldspar, and biotite. The minor minerals are titanite, calcite, cancrinite, and sodalite. Trace minerals are the niobium- or rare earth element-rich minerals pyrochlore, columbite, euxenite, britholite, ancylite-Ce and wöhlerite. Apatite, rhodochrosite, strontianite, fluorite, zircon, magnetite, ilmenite, and pyrite occur as traces as well. Crystallization started with primary (magmatic) calcite and Nb-rich minerals pyrochlore, columbite, euxenite, and a first generation of apatite, which occur as inclusions in foids, feldspars, and Fe-rich clinopyroxenes. Calcite is enriched in light rare earth elements and Sr, with low Mg concentrations, while primary apatite has high Sr concentrations. Both minerals have a composition typical for minerals crystallized in carbonatites. The presence of calcite and high Fe and low Ti clinopyroxene point to CO2-saturated conditions. During cooling, fluorbritholite-Ce formed as individual grains or by a fluid-enhanced apatite-britholite transformation. The formation of Fe-rich amphibole, often at the expense of Fe-rich clinopyroxene, reveals a decreasing influence of CO2 and temperature. Presumably, the transformation of orthoclase into microcline occurred simultaneously. Perthitic microcline as a second K-feldspar generation indicates slow cooling from high temperatures. A late stage of CO2-rich hydrothermal-metasomatic processes is suggested by the growth of secondary cancrinite, Sr-Mn carbonates and ancylite-Ce. The composition of primary and early crystallized calcite and apatite makes their origin as residues of an early segregated or independently formed mantle-derived carbonatitic melt more likely than crystallization from a CO2-rich syenitic melt. An origin from melted crustal carbonates is unlikely as well. Therefore, the presence of a carbonatitic melt at an early magmatic evolutive stage, as opposed to a non-carbonatitic melt at a late stage, seems possible for the SJGS rocks.