During the last 10 kyr, significant subsidence and uplift occurred on Mayotte Island in the Comoros archipelago (Indian Ocean), but the role of volcanic processes in Holocene vertical movements has been neglected in the research so far. Here, we show that an abrupt subsidence of 6–10 m occurred between 9.4 and 10 kyr ago, followed by an uplift of the same amplitude at a rate of 9 mm/yr from 8.1 to 7 kyr ago. A comparison of the relative sea level of Mayotte and a reference sea level curve for the global ocean has been conducted using a modeling approach. This shows that an increasing and decreasing pressure at depth, equivalent to the process caused by a deep magma reservoir (50–70 km), was responsible for ~6–10 m subsidence and 6–10 m uplift, whereas loading by new volcanic edifices caused subsidence during the last few thousand years. Surface movements and deep pressure variations may be caused by pulses from the deep mantle, related to superplume activity, but uncertainties and unknowns about these phenomena are still present and further studies are needed. A better understanding of the volcano-tectonic cycle may improve assessments of volcanic hazards.