Messi netted two goals and set up one more in a 3-1 victory over second-tier Girona on Wednesday, Barcelona's second training match since Koeman took over as coach.
The goals were also Messi's first since his failed attempt to leave the club this offseason, following a trophy-less season and the humiliating 8-2 loss to Bayern Munich in the Champions League quarterfinals. Messi told the club he wanted to leave, only to change his mind after Barcelona refused to allow him to go.
Barcelona posted a photo on Twitter of Messi and Koeman clasping hands when the star forward was substituted along with most of his teammates with half an hour to go. It seemed meant to deliver a message of unity between the player and manager amid one of the most tumultuous periods in the clubs recent history.
Barcelona is trying to find new homes for Suarez and Vidal, two players who at 33 years old do not fit into Koeman's plans to rejuvenate the team.
Spanish media reported that Vidal is close to a move to Inter Milan. Juventus reported interest in Suarez appears to have cooled in recent days.
Girona offered little resistance to Barcelonas attack, formed by new signing Francisco Trinco, Philippe Coutinho, Antoine Griezmann and Messi.
Messis perfectly placed pass sent Trinco clear for the Portugal forward to square the ball to Coutinho, who only had to scoop in the 20th-minute opener.
Messi doubled the lead in the 45th with a shot from outside the area that went in off the upright.
Samuel Saiz got Girona on the scoreboard after halftime before Messi got his brace with a shot that took a deflection off a defender to fool the Girona goalkeeper.
Barcelona won its first friendly 3-1 against Gimnstic de Tarragona last weekend.
Koeman will have one more warm-up match against Elche on Saturday before Barcelona starts the Spanish league season against Villarreal on Sept. 27.