Messi stunned the world last month when he informed Barca of his intention to depart the LaLiga giants, with the 33-year-old intending to trigger a clause in his contract to walk away on a free at the end of last season.
However, the validity of such a stipulation was murky due to the campaign being extended by the coronavirus pandemic, and Messi ultimately opted to remain in Catalonia rather than challenge Barcelona in a legal battle.
That did not prevent him from taking aim at Bartomeu in an interview with Goal, though, as he accused the president of reneging on his wish to leave and presiding over a club that had "no project or anything for a long time".
"As president, I will not enter into any conflict with Messi," Bartomeu told TV3.
"Messi is our captain, our leader. The issue is parked. What has been said has been said.
"I couldn't allow to let the best player in the world go. The team needs him, he guarantees success. Things have to be discussed at home. You have to support the team and the players.
"We have to congratulate ourselves that Messi is still with us. He is excited about [coach Ronald] Koeman's project. The important thing is he plays for Barca, at his home. We want him to retire at the club."
Messi's contract expires at the end of the 2020-21 season anyway, though by that point Barcelona will have a different president as there are elections to replace Bartomeu next March.
However, Bartomeu, unpopular with some Barcelona fans due to his role in the Messi saga, may be forced out before then if he faces a vote of no confidence on the back of a motion to remove him, which has so far gathered more than 20,000 votes.
"Right now, no-one is considering resigning," Bartomeu added.
"The club is not going to stop. I think everyone was surprised by the number of signatures but we respect democracy and the club's laws."