But he was handed a chance to impress by Mourinho – once again against Swansea – in November and the Englishman hasn’t looked back, cementing himself as a first choice option alongside Eric Bailly this season.
And Jones, whilst not openly disparaging of Van Gaal, was quick to make note of who he considered to be a better manager at Old Trafford.
“I don’t want to disrespect the other managers I’ve played under because I have the utmost respect for all the managers I have worked for and their opinions,” he said.
“Whether you think they are right or wrong you still have the respect for them, but I just feel in general that Sam Allardyce, Sir Alex and Jose Mourinho are the managers that have made me feel so wanted at the club and need me as one of their main players.
“Any footballer would tell you that if that’s the case, then they are going to get the best out of you. I have seen comments [from Mourinho about wanting Jones at centre-half] and it’s nice to hear that from the manager, but I am under no illusions.
“Equally, when times are tough, I am not one for just throwing the towel in. It was difficult towards the end of the second season under [Louis] Van Gaal but sometimes your face fits, sometimes it doesn’t.
“I always said to myself that if I can be strong and mentally strong, I would have a chance under the new manager and thankfully he has given me that. Last season I didn’t start so well, but towards the back end of the season I played a lot of games, felt good, felt strong and I feel the same this season.”
“I’ve become more experienced as a player as I’ve got older. You need to be sensible on the pitch and sometimes I don’t need to go for balls I would have done five or six years ago. It’s just experience and having a better understanding of the game and who is around you.
“As a defender, you want to stop goals going in and so far at United, we have been able to do that. Some people would say we’ve not played Man City or Chelsea or Arsenal but there are no easy teams in the Premier League whether you play home or away, so it’s positive.
“We are not getting too carried away with things. We have a long way to go. I feel good, happy and strong. I want to keep playing and play as many games as I can this season.”
The tale of Jones reveals that, no matter how anonymous and on the fringes you may be, a return to prominence can always lie around the corner.
Sir Alex Ferguson was quick to lavish the raw talent and power offered by Jones at the back – that emphatically bullish, bruising style which unfortunately lends itself to a fair amount of collateral damage. But Van Gaal didn’t see it. He viewed Jones as too unreliable, a loose cannon without the necessary composure on the ball.
But Mourinho, as all good managers do, has extracted the finest aspects of Jones’ game and placed them at the forefront of his approach alongside the equally imperious Bailly.