Exposed plumbing systems provide important insight into crystallization and differentiation in shallow sills beneath volcanic fields. We use whole rock major element, trace element and radiogenic isotopic compositions, along with mineral geochemical data on 125 samples to examine the conditions of melt differentiation in shallow sills from the exposed 4-Ma-old San Rafael subvolcanic field (SRVF), Utah. The field consists of ∼2000 dikes, 12 sills and 63 well preserved volcanic conduits. Intrusive rocks consist of mainly fine-grained trachybasalts and coarse-grained syenites, which are alkaline, comagmatic and enriched in Ba, Sr and LREE. Within sills, syenite is found as veins, lenses, and sheets totally enveloped by the basalt. The SRVF intrusions have geochemical signatures of both enriched sub-continental lithospheric and asthenospheric mantle sources. We estimate partial melting occurred between 1·2 and 1·9 GPa (50–70 km), with mantle potential temperatures in the range 1260–1326 ± 25°C, consistent with those estimated for volcanic rocks erupted on the Colorado Plateau. Geobarometry results based on clinopyroxene chemistry indicate that (1) basalt crystallized during ascent from at least 40 km deep with limited lithospheric storage, and (2) syenites crystallized only in the sills, ∼1 km below the surface. San Rafael mafic magma was emplaced in sills and started to crystallize inward from the sill margins. Densities of basalt and syenite at solidus temperatures are 2·6 and 2·4 g/cc, respectively, with similar viscosities of ∼150 Pa s. Petrographic observations and physical properties suggest that syenite can be physically separated from basalt by crystal compaction and segregation of the tephrophonolitic residual liquid out of the basaltic crystal mush after reaching 30–45% of crystallization. Each individual sill is 10–50 m thick and would have solidified fairly rapidly (1–30 years), the same order of magnitude as the duration of common monogenetic eruptions. Our estimates imply that differentiation in individual shallow sills may occur during the course of an eruption whose style may vary from effusive to explosive by tapping different magma compositions. Our study shows that basaltic magmas have the potential to differentiate to volatile-rich magma in shallow intrusive systems, which may increase explosivity.