The Madeira and Desertas Islands (eastern North Atlantic) show well-developed rift zones which intersect near the eastern tip of Madeira (Sao Lourenco peninsula). We applied fluid inclusion barometry and clinopyroxene-melt thermobarometry to reconstruct levels of magma stagnation beneath the two adjacent rifts and to examine a possible genetic relationship during their evolution. Densities of CO2-dominated fluid inclusions in basanitic to basaltic samples from Sao Lourenco yielded frequency maxima at pressures of 0.57–0.87 GPa (23–29 km depth) and 0.25–0.32 GPa (8–10 km), whereas basanites, basalts and xenoliths from the Desertas indicate 0.3–0.72 GPa (10–24 km) and 0.07–0.12 GPa (2–3 km). Clinopyroxene-melt thermobarometry applied to Ti-augite phenocryst rim and glass/groundmass compositions indicates pressures of 0.45–1.06 GPa (15–35 km; Sao Lourenco) and 0.53–0.89 GPa (17–28 km; Desertas Islands) which partly overlap with pressures indicated by fluid inclusions. We interpret our data to suggest a multi-stage magma ascent beneath the Madeira Archipelago: main fractionation occurs at multiple levels within the mantle (>15 km depth) and is followed by temporary stagnation within the crust prior to eruption. Depths of crustal magma stagnation beneath Sao Lourenco and the Desertas differ significantly, and there is no evidence for a common shallow magma reservoir feeding both rift arms. We discuss two models to explain the relations between the two adjacent rift systems: Madeira and the Desertas may represent either a two-armed rift system or two volcanic centres with separate magma supply systems. For petrological and volcanological reasons, we favour the second model and suggest that Madeira and the Desertas root in distinct regions of melt extraction. Magma focusing into the Desertas system off the hotspot axis may result from lithospheric bending caused by the load of the Madeira and Porto Santo shields, combined with regional variations in melt production due to an irregularly shaped plume.