The U23s' unbeaten run came to an end on a windy afternoon in Suffolk.
With a much-changed side from the one that had beaten West Bromwich Albion to advance in the Premier League Cup last time out, the Clarets gave a first start at this level to striker Lewis Richardson.
And there was also a debut from the bench for Under-16 team-mate Ben Woods against a stronger and much more experienced Ipswich side who included first-team players Kayden Jackson, Andre Dozzell and Josh Emmanuel and banked the points with two first-half goals.
With the weather conditions playing a huge part in the opening 20 minutes and both teams having to adjust to Storm Freya, it was the Clarets who had the first real chance.