A Chebyshev polynomial discretisation method is used to investigate the effect of both anisotropic (radially and azimuthally) and isotropic surface roughnesses on the convective instability of the BEK family of rotating boundary-layer flows. The mean-flow profiles for the velocity components are obtained by modelling surface roughness with a partial-slip approach. A linear stability analysis is then performed to investigate the effect of roughness on the convective instability characteristics of the inviscid Type I (cross-flow) instability and the viscous Type II instability. It is revealed that all roughness types lead to a stabilisation of the Type I mode in all flows within the BEK family, with the exception of azimuthally-anisotropic roughness (radial grooves) within the Bödewadt layer which causes a mildly destabilising effect. In the case of the Type II mode, the results reveal the destabilising effect of radially-anisotropic roughness (concentric grooves) on all the boundary layers, whereas both azimuthally-anisotropic and isotropic roughnesses have a stabilising effect on the mode for Ekman and von Kármán layers. Complementary results are also presented by considering the effects of roughness on the growth rates of each instability mode within the Ekman layer.