Herein we report on the chemical and isotopic (C, H, O, and He) compositions of the fluids from La Fossa crater fumaroles of Vulcano from 1999 to 2010. Consistent with records obtained since the end of the 1980s, our data show that the geochemical features of the fumarole system have experienced several episodes of remarkable change, each lasting no more than a few months. Typical signatures of these short-term anomalies are large increments in CO2, N2, and He concentrations, coupled to increased 13C/12C isotopic ratios, but their meaning remains widely debated. Within a model of fumarolic fluids based on mixing between hydrothermal and magmatic endmembers, we have developed a novel approach to constrain chemical (He/CO2 and N2/He) and isotopic (13C/12C, D/H, and 3He/4He) ratios of the magmatic endmember during the short-term anomalies. Although much of the geochemical variability in fumaroles results from changes in mixing proportions, the magmatic fluid unquestionably shows significant variations in time. The magmatic He/CO2, N2/He, 13C/12C, and 3He/4He values throughout 1988–1996 differed from those feeding the anomaly at the end of 2004. Early clues of the new magmatic fluid appeared in 1998–1999, far from any short-term anomaly, whereas new and old magmatic fluids coexisted after 2004. We quantitatively prove that the detected geochemical changes are consistent with the degassing path of a magma having a latitic composition, and suggest the presence of two magma ponding levels at slightly different pressures, where bubble–melt decoupling can occur. The different He-isotope compositions at these levels suggest low hydraulic connectivity typical of a complex reservoir with dike and sill structures. In this framework, the short-term geochemical anomalies are probably due to gas accumulation at the top of magma bodies followed by massive escape, or activation of new degassing levels in the reservoir, for which the stress field almost certainly plays a key role. Such a scenario explains the observed increases in both fumarole output and shallow high-frequency seismicity (due to increased pore pressure) during the anomalies, while being consistent with the concomitant absence of any deep seismicity or ground deformation, eventually related to magma movement.