During his first season back at Stamford Bridge, Mourinho froze out Mata, who had won Chelsea's player of the season award for the past two years.
Mata was eventually sold midway through the season to United in a £37.1m move amid rumours of a bust-up between the pair.
However, speaking on the adidas X podcast, Mata has revealed he simply fell out of favour under Mourinho at Chelsea because "he had a different way of playing football".
He said: "At the time, it was a bit difficult because [things were great in] 2011/12 and then the next season, which probably was my best season in terms of numbers and games played and enjoying on the pitch, 2012/13.
"We won the Europa League at the end with Rafa Benítez as a coach and everything was going so well on a personal level.
"And then José arrived and he had a different way of playing football, or a way that was not perfect for my qualities as a player, and that was it. I was not playing much as I used to play before.
"There was never a personal problem between us, like some people said at the time, but it was a challenge for me.
"Having been Player of the Season for the last two years in a row, playing nearly 70 games [in 2012/13] and feeling like an important player of the group, everything changed and I had to prove myself again. I didn't last very long after that at Chelsea."
The two crossed paths again two years later when Mourinho took over as United boss, with Mata needing to prove his worth.
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He added: "I could see that, when he came to Manchester United at a different stage of my career, everyone was saying 'okay you have no future at the club, you're going to have to leave, whatever'. I was calm with myself.
"I know what I am as a player. I know my will to adapt, and I'm proud that time proved me right as I felt an important player at Manchester United.
"What I try to focus on is things I can control: my attitude, my qualities as a player, keeping my confidence high, keeping my physical state high, and that's it."