Barcelona made two offers for their academy graduate in the summer of 2010, only to be turned down on both occasions by Arsenal, and the subject of Fabregas' future has once again been in the spotlight given the two clubs are playing against each other in the Champions League.
While Fabregas said on Friday he is "committed" to Arsenal, Messi has joined team-mate Xavi in expressing the belief that the Catalan is planning to return to his boyhood club.
"Let's hope so," Messi told Sport. "In the end he will do what he wants and what the people at Barca want. It doesn't depend on us, but I think his inclination is to be at Barcelona because there is nowhere he will be better off than here."
Messi continued his run of failing to score against English sides in Barcelona's 2-1 defeat at Emirates Stadium on Wednesday, but scored four times at Camp Nou when the sides met in last season's competition at the quarter-final stage.
He believes Barca deserved better than their loss in North London and appears confident his side can overturn the deficit on March 8.
"It hurt to lose because we didn't deserve to," Messi said. "In the first half we played really well for a lot of the time, moving the ball around quickly - it's a shame we didn't win. But we are relaxed because we know we can turn this around - we only have to overcome a one-goal deficit.
"It doesn't matter how we do it. Whether it's with my goals or not, the most important thing is to go through. We have to play in the same way and if we play like we did in the first half, we will have a great chance of going through."