This work highlights the necessity of taking into account surface roughness when conducting experimental tests, and when using numerical simulations to precisely calculate the turbulent lift and drag of wind-tunnel models or real aircraft in transonic conditions. The present article is a continuation of “Turbulent drag induced by low surface roughness at transonic speeds: Experimental/numerical comparisons,” Physics of Fluids, Vol. 32, 045108 (2020) by Hue and Molton. The outcomes of this former study, which was focused on flat plate samples, are here applied to a three-dimensional aircraft configuration: the Common Research Model used as a reference in the recent international Drag Prediction Workshops. Experimental campaigns have been performed in the largest ONERA wind tunnels S1MA and S2MA involving models with average surface roughness heights Ra close to 0.5 micrometers, wingspans up to 3.5 meters, Mach and Reynolds numbers up to 0.95 and 5 million respectively. Reynolds-averaged Navier–Stokes computations based on the wind-tunnel tests have then been carried out, using the equivalent sand-grain roughness height approach as well as a Musker-type correlation to determine relevant ks values. The results of both the experimental and numerical campaigns have demonstrated that the aerodynamic coefficients of the aircraft can be significantly affected by the surface roughness, even with roughness Reynolds numbers ks+ potentially below the usual threshold values sometimes considered in engineering applications (i.e. in the order of 3.5 to 5). In particular, the surface roughness effects on lift and drag have been studied using far-field analyses to evaluate the responses of friction, viscous pressure, wave and lift-induced drag components. Finally, the numerical studies have been extended to the full-scale geometry in flight conditions in order to assess the roughness effects and potential gains in realistic aircraft operating conditions.