The Barcelona legend is yet to fully fire under his new coach at the club but was hailed by Koeman after threatening to leave the Spanish giants this summer.
He told Sport: "Messi has shown me to be a person who wants to win things and continue to be the best, even though he has had his problems with the club.
"Barcelona have been, are and will be a better team with Messi than without. When I arrived, they told me that Messi was unhappy.
"We spoke at his house and he explained his reasons to me. I was honest. I told him that the only thing is the system, his position on the field, his importance in the team."
The Dutch boss backed Messi to hit his usual goalscoring number despite his sluggish start.
Koeman said of the star: "He has had his issues, his problems this summer, but since he returned to training he has been very good.
"He has had bad luck in some games and he has not been able to offer the usual performance, but I am sure that at the end of the season he will have scored the usual goals."
Barca sit eighth in the La Liga table but Koeman suggests that poor refereeing has prevented them from gaining more points.
He said: "It is true that we have lost many points in the league, in games that we could have achieved a better result. Refereeing decisions have influenced the final result in some."