First-half goals from Kylian Mbappe, Jude Bellingham and Yan Diomande made it an easy outing for Los Blancos at the Estadio El Sardinero.
Victory maintains Mourinho's positive momentum after last weekend's 2-1 El Clasico win over Barcelona as his focus now switches to a midweek UEFA Champions League trip to AEK Athens.
Mourinho has won all three European games so far in 2026/27 - alongside nine from 11 in league action - and he dropped a big hint over who will not start in Greece.
"I left out on the pitch several players who will be on the bench on Wednesday. Tchouameni will not play, for example.
"This is how I manage the players due to the amount of games we have."
Arda Guler, Bernardo Silva and Diomande were the three players taken off by Mourinho in Cantabria as a hint at his thinking.