Outcrop-scale structures and magnetic fabric anisotropy of the Bomdila Gneiss (BG) that intruded the Lesser Himalayan Crystallines (LHC) of the Arunachal Lesser Himalaya are studied to understand the BG deformation history and tectonic evolution. Detailed analysis of structures reveals that the LHC have undergone three phases of deformation, D1, D2 and D3. The S2 foliation developed during the second phase of deformation (D2) is the most penetrative planar fabric in the studied rock, which shows a general ENE–WSW strike with moderate NW dip. Mesoscopic evidence of a later phase of deformation (D3) in the BG is lacking. Evidence of D3 deformation in the form of F3 folds is only observed in the adjacent metasedimentary rocks of the LHC. The magnetic foliations recorded from anisotropy of magnetic susceptibility (AMS) analysis of the BG are mostly striking NW–SE with a moderate dip towards the NE or SW, and magnetic lineation is mostly sub-horizontal and dominantly plunging towards the SE. Our study shows that the magnetic fabric of the BG does not correspond to any visible outcrop-scale mesoscale foliation. However, the magnetic foliation of the BG is parallel to the axial plane of the F3 folds of the adjacent metasedimentary rocks of the LHC. Integration of AMS and outcrop-scale structural analysis helps us envisage the superposed deformation history of the BG. Our study emphasizes the importance of AMS to detect late-stage or feeble deformation events that leave no visible outcrop-scale imprint and are difficult to discern through conventional geological means.