But gradually the 23-year-old began to find his feet and, playing alongside Chris Smalling at the heart of the United defence, he has started their last three games with notable assurance.
"Coming here to play at this great club has been a dream for me since I was a kid, so yeah - I enjoy it every day", Lindelof told Sky Sports ahead of the Monday Night Football clash with Crystal Palace. I remember both of those periods very strongly. It's important to know how to play when the opponent is better than you.
"On both occasions I remember the enormous joy and satisfaction that the players and the whole club took, having overcome a very hard obstacle in front of them and come out the other side smelling of roses. This club is one of the biggest clubs in the world, so you're obviously going to have that".
"Every game is hard here", Lindelof said.
His shaky performances in pre-season and in training convinced Mourinho to limit the centre-back to only three appearances in the first two months of the campaign - and those came in the League Cup and two undemanding European fixtures. If you do get the ball from him he's going to be at you again to try and win it back, which is a very good quality, and he is experienced.
Paul Pogba, who has been the subject of much scrutiny recently, was amongst the players who travelled and the Frenchman was seen speaking to Mourinho at Stockport railway station.
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The 70-year-old has watched his team, undermined by a succession of injuries and the improving form of their rivals, return to the division's bottom three having already once fought their way to mid-table.
"The atmosphere in the dressing room has been really good and they have received me very well so we can talk a lot and get to know everyone".
"As a player, you always want to play games and that's what I've been doing over the last few games and I'm very happy that I can help the team on the pitch".
Mourinho's decision to grant an unusual request from his defender shows his trust of Lindelof extends beyond the football field.
"Of course, I think I've become a better player since I came here. I think I was pretty good, it was a fun time for me to go out on the ice and play with them!"