Deciphering deep magmatic processes driving the onset of continental break-up is fundamental to constrain our understanding of plate tectonics. The East African Rift System (EARS) represents the only opportunity to study a currently active system on Earth undergoing distinct stages of rift evolution. We present a coupled analysis of melt and fluid inclusions in the Virunga Volcanic Province (VVP) offering unprecedented insight into the dynamics of incipient rifting and its evolution. Our study highlights that melting of distinct metasomes in the deep lithosphere is a common feature of immature rifts. In the VVP, it leads to the emission of nephelinitic and basanitic melts at Nyiragongo and Nyamulagira volcanoes, respectively. Additionally, the chemical composition of melt and fluid inclusions supports the identification of another magmatic series in the area. We suggest that the related alkali basaltic melts were produced by contemporary melting of a less enriched domain in the upper lithosphere, a process that is more commonly documented in mature rifts. Various extents of mixing and crystallization of these three distinct magmatic series occur in the lower crust beneath the VVP where the barometric estimates are consistent with the presence of a thick seismic low velocity zone (LVZ). The involvement of alkali basaltic melts in the regional magma production would be also detected in the spread of gas emissions in the rift valley and in the fumaroles of the main active volcanoes. Melting of the corresponding mantle domain is an added source of gas release that may largely contribute to CO2 emissions along the EARS.