Messi, 33, will train individually for the next few days, per La Liga's strict coronavirus protocols, before reintegrating with his teammates at a later date.
Barca host Gimnastic in a friendly at the Johan Cruyff Stadium on Saturday, but Messi is not likely to be involved. He could feature against Girona in another friendly on Sept. 16 ahead of the season opener against Villarreal at the end of the month.
Messi felt he should have been allowed to leave for free due to a clause in his contract. However, when Barca put up barriers to prevent him from walking away, he conceded defeat and decided to stay to avoid a legal battle against "the club of my life."
As part of his push to leave, he was absent for the start of preseason under new coach Ronald Koeman last week. His legal team advised him that turning up for training for the new season would nullify the claim he could leave for nothing.
Messi accepted defeat on Friday, though, telling Goal he would not take the legal route to force a Camp Nou exit.
It is the first time he's been face-to-face with Koeman since the two held a meeting on Aug. 21. In the meeting, Messi told the Dutch coach of his desire to leave the club.
"Now I don't know what will happen," Messi said last week when he announced he was staying.
"There is a new coach and new ideas. That's good, but then we have to see how the team responds and whether or not it will allow us to compete at the top level. What I can say is that I'm staying and I'm going to give my best for Barcelona."
Despite committing to the club for the upcoming season, his long-term future remains up in their air. His contract is up next summer and he's free to negotiate with other clubs from January.
The upcoming presidential elections at Barcelona could play a major role in what he does next. Josep Maria Bartomeu cannot stand again and whoever replaces him will hope to convince Messi to sign a new contract.
Meanwhile, La Liga president Javier Tebas defended the league's decision to take Barcelona's side during the dispute over the clause in Messi's contract.
Messi's legal team asserted that the €700 million release clause was no longer active, while La Liga said they had analysed the contract and it was.
It led to an exchange between the player's father, Jorge Messi, and Tebas last week in which they both stood their ground.
"It wasn't a battle with Messi and his team," Tebas told Corriere della Sera. "I would have done the same if it had been any other player in the league.
"As a league, we must defend the rules and promote justice: [players] must respect their contracts. Always. Whether you're called Messi or Pepito Perez.
"I've got a special appreciation for Leo and the history he's created over the last 20 years. How could I be at war with him? I repeat, my intervention was only so that contracts were respected.
"Although his lawyers say the opposite, the contract is clear. I'm happy he will avoid a legal battle and continue playing for the club of his dreams."