The coupling of helium isotopes in fluid inclusions with conventional geochemical data provided a new perspective on the volcanic processes that took place during the Cretaceous in southern Sicily. Our new investigations reveal that during two distinct volcanic phases in the Late Cretaceous, magmas formed from low degrees of partial melting of a heterogeneous mantle source characterized by spinel lherzolite and varying garnet content. The collected samples, including lava flows, dikes, and sills, exhibit a wide range of rock types, from picritic basalts to hawaiites. Two different magma types were identified: one displaying a bell-shaped pattern akin to ocean island basalts (OIB) and another with an irregular pattern marked by positive spikes in Nb, K, Pb, Sr, Zr, and Ti. Strontium and Neodymium isotope compositions are weakly radiogenic, while the Pb isotope systematics show strong radiogenic values (206Pb/204Pb = 19.64–20.42; 207Pb/204Pb = 15.61–15.70; 208Pb/204 Pb = 39.26–39.98), corresponding to the mantle focal zone (FOZO) component. The observed 3He/4He ratios of 3.48 to 6.48 Rc/Ra in pyroxene fluid inclusions reflect the occurrence of pre-eruptive processes such as diffusion-induced fractionation or diffusive exchange taking place during magma residence in the crust. The 3He/4He ratios from 7.75 to 9.31 Rc/Ra in olivine crystals are typical of MORB-type basalts, and they likely represent the original signature of the mantle source. The olivine Rc/Ra values may indicate an interaction with recycled (U+Th)-poor lithologies or high 3He/4He materials in the upper mantle source. Furthermore, the 3He/4He isotope ratios of olivines differ from those determined in the same region for Plio-Pleistocene volcanic products, for which a common origin has been suggested in the majority of previous studies. In light of our findings, the hypothesis that the Hyblean Late Cretaceous and Plio-Pleistocene volcanics are part of a single magmatic suite should be reexamined. Overall, our results indicate that the evolution of those volcanic rocks was influenced by fractional crystallization and accumulation processes providing additional details on the mantle source that may have been overlooked in the past.