Abstract We used quantitative textural measurement, electron microprobe microanalysis and thermobarometry on clinopyroxene from a Cenozoic pyroxene-nephelinite flow located along the northern boundary of the West African craton to decipher magma differentiation processes in underlying magma chambers. The crystal size distributions of clinopyroxene phenocrysts show straight but also curved and kinked patterns and the clinopyroxene show large compositional variations in a single flow (Mg-number 48–88). These observations are strong evidence for magma mixing between a nephelinite magma and a more differentiated phonolitic melt at depth. Detailed thermobarometry on these clinopyroxene shows that at least three magma chambers are present below Saghro and that they are emplaced at the main physical interface within the lithosphere: (1) at the crust–mantle boundary, where the mantle-derived nephelinite has been mixed with a pre-existing phonolitic magma chamber; (2) at the lower–upper crust boundary; (3) close to the surface in a sub-volcanic magma chamber. Some high-pressure phenocrysts (up to 14 kbar) have also probably crystallized within the upper lithospheric mantle. The high clinopyroxene proportion in samples from the base of the flow is thought to reflect crystal settling during cooling of the nephelinite flow at the surface.