The Koillismaa–Näränkävaara Layered Igneous Complex (KLIC) has been the subject of continuous studies due to its potential to host several critical raw materials, mostly of the Ni-Cu-PGE sulphide type. The KLIC is characterised by a ~50–60 km-long geophysical anomaly in which the magnetic high is followed by a shifted gravity high response, believed to be caused by the Koillismaa Deep Intrusion (KDI), but the exact origins remain unknown. A regional reflection seismic profile was acquired under the SEEMS DEEP project (2022–2025) to define the spatial geometrical architecture of the KDI. Initial processing using standard time-domain and conventional depth imaging revealed its first-order large-scale structure, indicating a funnel-shaped geometry and confirming it as a geologically complex target. In this study, we apply advanced seismic imaging methods, better suited to complex geologies, to further improve the imaging of the KDI. Ray-based (least-squares)Kirchhoff prestack depth migration and wave-equation-based reverse time migration (RTM) were used for this purpose. A high-resolution P-wave velocity model was built using acoustic full waveform inversion (FWI), while first arrival traveltime tomography was applied to build the starting model for FWI. Wave-equation-based, joint RTM-FWI workflow provided the optimum imaging of the KDI setting. A comprehensive reinterpretation of the KDI was done using the multi-method approach integrating gravity, magnetic and electromagnetic surveys. The available borehole information and common earth model for the study area were used as constraints. Shallow seismic reflectivity correlated well with the mafic dykes observed in the magnetic data. The exact origin of these dykes was earlier unknown and was attributed to the observed magnetic high in the KLIC area. Advanced seismic imaging revealed a previously unrecognized, more laterally extensive top of the KDI whose full extent was previously unknown. It is also interpreted that the denser mafic intrusion (KDI) defined by this extensive top may have increased the net vertical mass distribution in the area, because of which a shifted gravity response with respect to the magnetic high has been observed. A new hypothesis on the angular ascent of the magma towards the surface is also proposed based on the mapped seismic reflectivity associated with the mafic intrusion.