In the present work, we investigate the effect of conical roughness on heat flux and coherent structures for Rayleigh number Ra=108 in a three-dimensional (3D) cubic cell filled with air. Two roughness setups are explored, and unlike the uniform case, height of the conical elements varies as 50−100% of the maximum roughness height for the irregular case. In addition, we also study their half-variants, i.e., half-uniform (HU) and half-roughness (HR), where the rough surface is considered only on the bottom plate. While heat flux increases significantly in the rough cases, roughness weakly impacts the flow strength. The heat flux increases due to emission of a large number of intense thermal plumes, which is confirmed by an increase in plume volume fraction Vpl. Larger temperature variance in the rough cases confirms the frequent emission of thermal plumes. A shift in mean temperature in the bulk region is observed for HU and HR cases due to a surge in hot plumes emitting from the rough bottom surface. Large-scale circulation (LSC) remains in the diagonal plane in the smooth case, whereas it is found aligned along the Cartesian planes in the rough cases. The strength and orientation of the LSC are quantified by Reynolds number based on angular velocity. In the plane of LSC, we also obtain greater local heat flux in rough cases. Power spectra of temperature fluctuations reveal the existence of Bolgiano–Obukhov (BO59) scaling in the bulk region.