The Buckinghamshire side created a number of good chances throughout the first half, but were continually thwarted by the outstanding ability of Pompey’s loanee goalkeeper, Gavin Bazunu.
However, during the second half Danny Cowley’s side were very much in the ascendancy and conceded against the run of play as the Dons executed a perfect-counter attack to take the lead with 20 minutes remaining.
Manning recognised the ability in the Pompey squad, and praised the way the Blues played in the second half.
Manning said: “It was a really tough game against really difficult opposition. In the first half, we were terrific, created some really good chances and looked really dangerous throughout the game. We could have controlled possession a bit more but it was disappointing not to go in ahead at half time.
“But that flipped in the second half - they got on top when we couldn't get our press right. What it shows is even when we're up against it, the quality we have throughout the team, we can go and hurt people.”
The 36-year-old was appointed as Dons chief on the eve of the season after former boss Russell Martin’s shock departure to Swansea City. After the victory against the Blues, Manning’s side have leapfrogged their opponents and climbed to fifth place in the League One table.
The Dons have now won three of their opening seven matches under Manning, while drawing three, and only losing once. Arguably their triumph over Pompey is their biggest scalp under the former Lommel boss.
Manning has become the first ‘head coach’ in MK Dons history, but after their good start to the season, isn’t getting carried away just yet.
Manning concluded: “There's a long way to go - it's important not to get carried away or get ahead of ourselves. It's really important to stay grounded, focus week-to-week on what we can control so when we go into next week, we're better than we were last week and today.