The prolific forward has erased Paulino Alcantara's name from the record books following his goals against Osasuna.
The Argentina international already became the top goalscorer in the club's history in official matches two years ago, erasing Cesar Rodriguez from the record books, but Paulino Alcantara's number had stayed out Messi's reach until this weekend's encounter.
Alcantara, born in the Philippines, scored 369 goals in 357 games as a Barca player between 1912 and 1927, but the Blaugrana legend has now been overtaken by Messi.
The 26-year-old has been in sublime form in 2013-14, netting 17 goals in 21 La Liga encounters.
The prolific attacker's next objective is becoming the top goalscorer in the history of the Champions League.
That honor is currently in the possession of Real Madrid icon Raul Gonzalez, who has scored 71 goals against Messi's 67.