Pompey went close to exiting the Papa John’s Trophy in both the group stages and their second round tie against Exeter.
But the luck finally ran out at Cambridge, who secured a 2-1 win to secure a visit to Rotherham in the quarter-finals.
The damage was done when Harvey Knibbs struck twice early in the second half, with Michael Jacobs’ header not enough to spark a comeback.
And Danny Cowley is looking for his side to show more consistency in their performances ahead of a busy run of league fixtures.
The Blues boss said: “It was frustrating and disappointing in equal measure because we find ourselves out of the competition. I don’t think we did enough.
“We got some good control in the first half after a difficult way into the game and were in the ascendency without creating as many chances as we would like.
“But it’s the second time in as many games where our intensity as dropped after the break and that’s ultimately what cost us.
"We need to find a 90-minute performance and show a bit more consistency because we’ve had good periods, but need to dominate throughout."
“There was a 15-minute period when we lost control and they scored two goals, so we have to look at that.
“We could have moved the ball quicker than we did and had more penetration in the box, although it was a well-worked set-piece for our goal.
“Credit to Cambridge, who are a honest and hard-working group – it was no surprise to me that they beat a Premier League side at the weekend.
“There’s a lot to like about the way they backed that up against us a few days later with grit, endeavour and enthusiasm.
“We’ve now had three games which have been like a mini pre-season for us after 23 days without a match.
“Now we need to find a 90-minute performance and show a bit more consistency because we’ve had good periods, but need to dominate throughout.”
Clark Robertson played the first half at Abbey Stadium, while Ryan Tunnicliffe was given half-an-hour after the break following long injury lay-offs.
Cowley said: “They were two big positives for us and they would have benefitted from that, while Louis Thompson also got another hour.”