The former Blues target played a central in ending the 10-game unbeaten run of Danny Cowley’s men, as his side picked up a 2-1 success on Saturday.
Eisa was pursued hard by Kenny Jackett in 2019 before opting to join Bristol City from Cheltenham.
The 27-year-old moved on to MK Dons last summer and has bagged seven goals so far this season.
Eisa gave Pompey a lesson in opportunism as he snaffled his first sight of goal in the 20th minute - on an afternoon where the home side rued wasted chances.
Manning told MK Dons’ official site: ‘With Mo there, in terms of one the shoulder, that’s his game.
‘It was a terrific shift and and terrific finish.
‘I was really pleased with Mo, because he had a tough couple of games and he openly admitted it.
‘What’s got him through that is looking to learn, looking to get better and working hard.
‘How he led the line, the work he put in - he sets the tone defensively as well. That’s important to recognise.
‘I’m really pleased for Mo and it’s a really good finish.’
Manning acknowledged his side had to show resilience and weather Pompey pressure to emerge victorious at Fratton Park.
He added: ‘That was everything that has to underpin our culture - work, fight, sticking together in tough moments. It's a terrific result and performance for so many different reasons for the ones we're usually associated with.
‘You won’t come to places like this and dominate for 95 minutes. It was always going to be difficult coming out in the second half, even though we were 2-0 up because of the atmosphere and the quality they have. We knew they'd increase their intensity, play direct and forward.
‘They dominated the second half but the score line played a part in that. But we dug in, defended the lead and it was a bit of a false reflection of what it looked like. But I'm delighted with what I saw in the second half.
‘You have to expect it when you come to somewhere like that.
‘You’re not going to come to somewhere like this and dominate for 95 minutes.
‘We knew we had to get through the first 10 or 15 minutes, and I thought we shifted the momentum really well back to us.
‘They started well, got on top and we caused some of our own problems with our sloppiness.
‘But after 20 minutes I thought we really got hold of the game and showed some quality with the ball.’
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