Los Blancos and Kylian Mbappe may have struggled in Europe this season, but the Frenchman looked bright from the beginning and collected Brahim Diaz’s pass before firing into the bottom corner just 10 minutes into proceedings for his 50th Champions League goal.
He then raced through again shortly after before seeing a venomous strike stopped by Marco Carnesecchi.
Ademola Lookman asked questions at the other end, with a shot being blocked by Aurelien Tchouameni and a low cross for Charles De Ketelaere forcing a vital intervention from Antonio Rudiger.
Wderson became the latest player to have a shot blocked by Tchouameni and Lookman struck wide as La Dea stepped up their search for an equaliser.
There was soon disappointment for Real Madrid, however, with Mbappe being forced off injured in the 36th minute before Rudiger headed wide from a golden opportunity to double his side’s lead.
The centre-back’s frustrations were compounded when his partner Tchouameni tripped Sead Kolasinac to concede a penalty that De Ketelaere emphatically converted with the last kick of the half, especially as the German had previously exchanged heated words with the forward.
Buoyed by that moment, Atalanta showed intent after the restart with De Ketelaere rising above Rudiger but heading wide before Lookman forced Courtois into a save with his strike from range.
They were behind in the 57th minute, though, as the ball bounced off Ederson and fortuitously fell to Vinicius Junior, who made the absolute most of it with a clinical finish.
Just three minutes later, Jude Bellingham cut inside Marten de Roon and beat Carnesecchi to give his side a buffer.
Lookman swiftly offered a reminder that Atalanta weren’t out of the contest, smashing his shot through Lucas Vazquez’s legs and out of Courtois’ reach.
Diaz and Rodrygo wasted a chance apiece to regain some breathing space, but Courtois denied substitutes Lazar Samardzic and Mateo Retegui before the latter missed the target from a golden opportunity as Real Madrid saw out a vital win in response to their previous back-to-back Champions League defeats, going 18th in the standings for now.
They also inflicted Atalanta’s first European loss this term, although La Dea are still currently ninth.
Flashscore Man of the Match: Jude Bellingham (Real Madrid)
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