Mourinho also managed the pair at Manchester United.
“We [Mkhitaryan] won together three titles [Community Shield, League Cup, Europa League] at Man United, unfortunately the last three titles of Man United. I say 'unfortunately' because, yes, I like the club very, very much and I wish the club the best," said Mourinho.
“We won three titles together so everything went well. In the second season, we were together was a little bit different. The thing that makes me really happy was because in the beginning, people try to go on a negative and say, 'Miki with Jose has no chance, Jose is the kind of guy when things go wrong never go well again', it was proven exactly the opposite. We were very mature, honest with each other at that time even with Mino (Raiola), rest in peace Mino, the discussion was very good.
“I try always to be very honest with the players. I saw my project in Rome needing a player like Miki, I also understand the importance of Miki in the group and he's having an amazing season.
“I am so happy with Miki and I'm happy with people understanding with me not everything is black or white. It's possible that a player comes with a different relationship than it was in the past."
Like Mkhitaryan, Smalling has also shone under Mourinho this season.
“With Chris, it's about finding a balance on his body that allows him to be playing regularly," said Mourinho.
“He's experienced, his know-how and his qualities as a defender as there. Also tactically in relation to the system the team plays and the defensive organisation.
“Chris is doing very well this season, playing at a level that makes me really happy about him because he is a fantastic player. He's recognised in Italy as 'Smalldini', half Smalling, half (Paolo) Maldini. He's doing amazing for us."