The French striker, who missed the last session before the midweek cup tie due to a dental procedure and did not travel to San Sebastian, joined the group for a full session with no issues.
Mbappe is now setting his sights on Real Madrid's next match, a trip to Real Betis on Saturday. The 26-year-old put in a tough shift alongside other players who were rested for the recent cup win against Real Sociedad.
He wasn't the only one given a breather - Thibaut Courtois and Federico Valverde also sat out that game, and both are expected to slot back into Carlo Ancelotti's starting line-up at the Villamarin.
Ancelotti will welcome back these three key starters after a short rest to recharge for a busy period ahead, but the Italian boss still has injury headaches to deal with. The latest blow comes for Dani Ceballos, who not only misses out on a return to his former club Betis this weekend but now faces around two months on the sidelines.
Add to that the suspended Jude Bellingham, and the list of absentees grows with Eder Militao, Dani Carvajal, and Jesus Vallejo already ruled out.
Ancelotti has said in the past about Mbappe: "He's a special talent, and when he's fit, he lifts the whole team."
The manager will be banking on that spark against a tricky Betis side, though fans are buzzing about how the squad will cope with so many big names missing.