Barcelona will always be the “first and best option for all players”.
His comments have come at a rather difficult time for the club, who are facing a possible legal battle to keep hold of six-time Ballon d’Or winner Messi amid interest from Manchester City.
Although he never had the same issues as his Argentina colleague in relation to the hierarchy, his praise for his former side is unlikely to go down well with the Argentine, as well as the outgoing Luis Suarez and Arturo Vidal.
"The first option and the best option for all players is always Barca," he told reporters after his exit was confirmed, before suggesting that it might not be the case for everyone.
"Then, each player has to make their decision. For me, the first option would always be to be at Barca.
"Every player has to do his own analysis and I believed it was my moment. What Messi and other players are going to do, I don't know, you'd have to ask them.
"I've spoken with the board and we're all satisfied. And I'm convinced that everyone will make their own analysis and do the best for all parties.
"I respect the decision of every player and I've already said that these are decisions everyone has to make."
The 32-year-old went on to insist that it is not the end of an era for Barcelona, despite the change in management, upcoming change in presidency as well as a likely first-team shake up.
"I've not said anything about the end of a cycle, only that I always analyse everything and the situation has arrived to start thinking in another way," he said.
"It's not the end of an era. After six years, it wasn't easy for me to leave. I'm really grateful for every detail.
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"I don't like to talk about the end of an era. I believe every player has to think about when the moment comes for them to leave, and that moment has come for me, nothing more."
Koeman said of Messi’s future last week: "I have to make sure he's able to function well in this team.
“I have to make sure he feels important. He's the captain of this club. He has to finish his career here. Messi is Barcelona and Barcelona is Messi."