The continued seismicity in Koyna–Warna region of the western part of Maharastra (India) and its relationship with subsurface structures, concealed below thick volcanic sequences, are studied in detail using gravity field along with newly available deep scientific drilling results. This seismically active zone is marked by a large conspicuous negative gravity anomaly, the causes of which are yet to be fully understood. Recent findings from the boreholes drilled in the Koyna (Gupta et al. in Int J Earth Sci 104:1511–1522, 2015) and Killari seismic zones, both of which penetrated the thick Deccan volcanic cover and the underlying Archean crystalline basement, have motivated us to revisit the Bouguer gravity field over this region, using a newly developed finite element method of regional-residual separation. Our study reveals the presence of two thick low-density/low-velocity crustal zones below the Koyna–Warna region, the shallower one between 5 and 13 km depth and the deeper one between 35 and 43 km depth just above the Moho. Both of these zones appear to contain mantle-metasomatised and fractionated magmatic material, respectively. Interestingly, the hypocenters of all M ≥ 5 Koyna earthquakes occur within the upper low-velocity/low-density zone. We also suggest high-order crustal exhumation below this region, which led to the removal of the entire sedimentary and granitic upper crustal column. This process has brought denser mid-crustal lithological facies close to the surface. Quaternary uplifting and movement of fault blocks along the old as well as newly created fault planes seem to be still continuing. A paleo-rift may have existed beneath this region below which Moho temperatures (~600 °C) and mantle heat flow (~31 mW/m²) are still high.