The Bonga complex is composed of a central carbonatite plug (with a ferrocarbonatite core) surrounded by carbonatite cone sheets and igneous breccias of carbonatitic, fenitic, phoscoritic and lamprophyric xenoliths set in a carbonatitic, lamprophyric or mingled mesostase. To reconstruct the dynamics of the complex, the pyrochlore composition and distribution have been used as a proxy of magmatic-hydrothermal evolution of the complex. An early Na-, F-rich pyrochlore is disseminated throughout the carbonatite plug and in some concentric dykes. Crystal accumulation led to enrichment of pyrochlore crystals in the plug margins, phoscoritic units producing high-grade concentric dykes. Degassing of the carbonatite magma and fenitization reduced F and Na activity, leading to the crystallization of magmatic Na-, F- poor pyrochlore but progressively enriched in LILE and HFSE. Mingling of lamprophyric and carbonatite magmas produced explosive processes and the formation of carbonatite breccia. Pyrochlore is the main Nb carrier in mingled carbonatites and phoscorites, whereas Nb is concentrated in perovskite within mingled lamprophyres. During subsolidus processes, hydrothermal fluids produced dolomitization, ankeritization and silicification. At least three pyrochlore generations are associated with late processes, progressively enriched in HFSE, LILE and REE. In the lamprophyric units, perovskite is replaced by secondary Nb-rich perovskite and Nb-rich rutile. REE-bearing carbonates and phosphates formed only in subsolidus stages, along with late quartz; they may have been deposited due to the release of the REE from magmatic carbonates during the hydrothermal processes.