In 2011–2012, Santorini was characterized by seismic-geodetic-geochemical unrest, which was unprecedented since the most-recent eruption occurred in 1950 and led to fear an eruption was imminent. This unrest offered a chance for investigating the processes leading to volcanic reactivation and the compositional characteristics of involved magma. We have thus analyzed the He-Ne-Ar-isotope composition of fluid inclusions in olivines and clinopyroxenes from cumulate mafic enclaves hosted in cogenetic dacitic lavas of the 1570–1573 and 1925–1928 eruptions of Nea Kameni. These unique data on Aegean volcanism were compared with those of gases collected in quiescent periods and during the unrest. The ³He/⁴He ratios (3.1–4.0 Ra) are significantly lower than the typical arc-volcano values (R/Ra ∼ 7–8), suggesting the occurrence of magma contamination in Santorini plumbing system, which would further modify the ³He/⁴He ratio of parental magmas generated in the local metasomatized mantle. The ³He/⁴He values of enclaves (3.1–3.6 Ra) are comparable to those measured in gases during quiescent periods, confirming that enclaves reflect the He-isotope signature of magma residing at shallow depths and feeding passive degassing. A significant increase in soil CO₂ flux from Nea Kameni and anomalous compositional variations in the fumaroles were identified during the unrest, accordingly with previous studies. Simultaneously, ³He/⁴He ratios up to 4.0 Ra were also measured, demonstrating that the unrest was due to the intrusion into the shallow plumbing system of a more-primitive ³He-rich magma, which is even volatile richer and less contaminated than mafic magma erupted as enclaves. This new intrusion did not however trigger an eruption.