Molybdenum (Mo) is a key material for several products in medicine and power electronics. Welding is crucial since without it many structures would cease to be in existence and industry requires continuously new joining processes to fulfill requirements of new materials. Friction welding is a solid-state technique for joining materials by frictional heat and the rotary friction welding (RFW) is the most common variant with no clear understanding of physical processes when applied to Mo-based alloys. Residual strains in these alloys are key outputs to assess the quality of the welding process modelling. This work aims at evaluating their residual strains for the first time for a more reliable modelling and understanding of the RFW process. This knowledge will be transferred to an industrial scale with its subsequent technological impact.