The abyssal Ionian Sea is a deep region of interest for the entire ocean circulation of the Mediterranean Sea, since it plays an important role in the ventilation processes of the whole basin. Here we investigate spatial patterns of diapycnal mixing due to internal waves, over the bottom of the Ionian sub-basin. To identify regional features of the internal wave field in terms of vertical shear and strain, we analyze LADCP and CTD profiles, measured across the basin in 2007, covering various seafloor morphologies (shelf, shelf break, and abyssal plain). Our results show that increasing seafloor roughness reduces the variability of the shear-to-strain ratio, a pattern also influenced by correlations between slope and roughness. Roughness appears to constrain waves toward higher frequencies, with high shear-to-strain ratios associated with lower frequencies and flatter propagation angles, and low ratios linked to higher frequencies and steeper beams. Spectral analyses indicate that rougher regions enhance strain variance at small vertical scales while reducing shear variance at larger scales, leading to flatter shear spectra in the low-wavenumber band. Together, these findings suggest that roughness redistributes energy from large-scale toward small-scale, fundamentally altering the balance of internal wave energy across scales. These results expand our insights for 3D ocean circulation models, providing useful knowledge for ad hoc parameterization of mixing that should capture abyssal, internal wave–driven processes in the Mediterranean Sea.