A vast portion of the plumbing system of the Siberian Traps Large Igneous Province (STLIP) is emplaced in the Tunguska Basin, where borehole data reveal ubiquitous and abundant sills with great lateral extension. These intrusions intersect Cambrian–Ordovician evaporite, carbonate and siliciclastic series, and locally coal-bearing Permian host rocks, with a high potential for thermogenic gas generation. Here we present new geochemical data from 71 magmatic and 4 sedimentary rock samples from the Tunguska Basin center and periphery, recovered from 15 deep sills intercepted by boreholes. The studied samples are all low-Ti basalt and basaltic andesites, confirming absence of high-Ti and alkaline STLIP magmatism in the Tunguska Basin. The sills derive from picritic parental melts produced by extensive melting of a mantle source with recycled crustal components below a thinned lithosphere (50–60 km), within the spinel stability field. The mantle source was dominantly peridotitic, with enriched pyroxenitic domains formed by recycled lower crust, in agreement with previous models for the main tholeiitic STLIP phase. Limited amounts (up to 5%) of highly radiogenic granitoids or moderately radiogenic metapelites were assimilated in upper crustal magma reservoirs. After emplacement, sills intruded in Cambrian evaporites assimilated marlstones and interacted with the evaporitic host rocks, probably via fluids and brines. This is the first time that such process is described in subvolcanic rocks from all across the volcanic basin. The sills are correlated geochemically with the established chemostratigraphy for the on-craton STLIP lava piles and intrusions (Norilsk region). Sills correlated with the Morongovsky–Mokulaevsky Fm. and the Norilsk-type intrusions are the most voluminous, present all across the central Tunguska Basin, and bear the strongest evidence of interaction with evaporites. Massive discharge of thermogenic volatiles is suggested by explosive pipes and hydrothermal vent structures throughout the Tunguska Basin. We propose that this voluminous pulse of magmatism is a good candidate for the hitherto unidentified early intrusive phase of the STLIP, and may link the deep Tunguska basin sills to the end-Permian environmental crisis.