Santorini volcanic complex (Greece) is the result of a long evolutionary history, marked by the alternation of explosive (Plinian) eruptions and interplinian low explosive/effusive eruptive cycles. Products emitted during the interplinian stages are well exposed along the rim of the calderic structure formed during the major Minoan (3.6 ka) Plinian eruption. We conducted a systematic sampling of the basaltic to dacitic lavas erupted by the interplinian volcanic centre of Skaros, active between 67 and 54 ka. The continuously exposed products of the Skaros lifecycle offer the tremendous opportunity to reconstruct the petrological evolution of the volcanic centre, and in turn to provide new insights on the behaviour of Santorini feeding system during interplinian stages. The combination of whole-rock, mineral chemistry and synchrotron X-ray computed microtomography analyses enabled us to decipher the main physico-chemical parameters of the Skaros plumbing system that drove ascent and differentiation processes of magmas. Results indicate that the main magma ponding zone beneath Skaros centre extended from 12 to 4 km b.s.l., where it underwent frequent refilling by basaltic melts. In the later evolutionary stage of the Skaros system, the basaltic replenishment became less frequent allowing the ultimate differentiation of magma towards dacitic composition. The shallow nature of the magma ponding zone, sited well above the H2O saturation depth, favoured the continuous degassing and inhibited the increase of vapor pressure during differentiation, preventing the onset of explosive eruptions, as in case of the major explosive events at Santorini. •Skaros volcano (Santirini) inter-Plinian effusive activity products were investigated.•The polybaric plumbing system was frequently fed by basaltic melts at early stages.•Magma feeding decreased in the late stage of the volcano activity.•Emitted lavas evolved towards more acidic composition.•Shallow depth of ponding zones favoured degassing, preventing explosive eruptions.