Ponding conditions of basalts erupted from fissure zones at São Miguel Island (Azores) were investigated through microthermometry of fluid inclusions, hosted in olivines and clinopyroxenes, and whole-rock and mineral chemistry. The Região dos Picos and Achada das Furnas fissure zones formed between central volcanoes and erupted geochemically similar magmas for the last 30 kyr. Hydrocarbonic fluid inclusions that survived to diffusion and re-equilibration recorded a maximum density value of 1000 kg m⁻³ (29.3 km) at both fissure zones, at the intersection with the feeding systems of older central volcanoes. The maximum density decreases to 875 kg m⁻³ (23.5 km) towards the central segment of Região dos Picos. Further trapping of low-density fluids is occasional and limited to a few samples. While the deepest event is interpreted to mark the vertical variation of the Moho at each location, all other events are only representative of short-time ponding with fluid re-equilibration. The deepening of the Moho towards the central volcanoes might be the effect of long-lasting underplating. However, the periodic stretching of the lithosphere, in response to the differential stress field acting at central volcanoes, would have been responsible for the thinning of the crust at the central segment of the fissure zone.