The Pompey boss has accepted he underused the mercurial talent this term, as he attempted to deliver a play-off finish.
Cowley has explained the circumstances behind the 30-year-old’s limited playing time across the first half of the season.
That was a source of frustration to many fans, before Jacobs came to the fore when given an extended run of minutes in the new year.
Cowley gave the background to his thinking over not giving the former Wigan and Wolves man more playing time.
But, speaking to the Three Lads in the Pub podcast, he stressed he felt it was necessary to show honesty when not getting decisions right.
Cowley said: ‘We probably underused Michael - that’s the truth.
‘He was a month behind the rest of the group because he’d had the knee operation in April.
‘He was chasing his fitness when the games around in the Papa John’s Trophy, and he wasn’t at 100 per cent match fitness.
‘So he didn’t do as well as he would normally have done.
‘Sometimes you don’t get everything right, that’s the reality.
‘For Nicky (Cowley) and myself, when you get it wrong you have two choices - you can look in the mirror or out of the window.
‘For us, it’s to look in the mirror when you make mistakes.
‘I always say to the players when I’m communicating, I always try to speak early with them.
‘The more difficult the conversation, the earlier I have it with them.
‘If I’m wrong, I try to tell them I’m wrong before they find me. That’s how I work.
‘With Michael, it took us too long to get to him.
‘There were reasons why, but ultimately that’s the reality - and we saw we were a better team with him over the second half of the season.’
It’s been a tumultuous season for Jacobs, who is one of the 12 players who are out of contract this summer.
A move to Ipswich collapsed last August, but Cowley is adamant that allowing that deal to take place wasn’t a reflection of their opinion on the attacking talent.
He added: ‘For us, we didn’t really want to lose Michael.
‘It was a good offer and we felt it was a good decision from a football and business point of view.
‘But then it didn’t happen and it’s been well publicised why.’