Prior to the Copa America final, which Argentina lost on penalties to Chile, Messi had lamented the AFA publicly, calling them 'a disaster' on social media.
The AFA is in crisis after it was reported that Argentina is on the verge of being disqualified from international football by FIFA after the world football governing body tried to take over the AFA after the AFA's president was accused of 'severe fraud' in regards to television rights deals.
Messi had said in the press conference before the final that he would "tell you (the media) everything" after the final.
Messi has since told the media that his time with the national team "is over".
Many outlets in Argentina are now reporting that Messi will be joined by numerous teammates in quitting the national team.
The AFA has long been a strange beast, but, since Julio Grondona's death brought his 35-year reign as president to an end in 2014, it has plunged into disarray.
Last December's shambolic presidential election drew the attention of the world when, despite there being 75 delegates present, a vote of 38-38 was counted.
Provisional president Luis Segura, who replaced Grondona, remained at the helm as the elections were pushed back, but opposing candidate Marcelo Tinelli has since pulled out.
With a permanent replacement for Grondona still not confirmed, elections scheduled for June 30 were postponed by the Argentinian government pending an investigation into the misappropriation of finances related to the national 'Futbol Para Todos' scheme.
This raised concerns that Argentina could be banned from competing at the Copa America Centenario, with government interference in football matters banned by FIFA.
And, on Friday, FIFA announced its decision to appoint a "normalisation committee" with a mandate that put it in charge of "running the daily affairs of the AFA, revising the AFA statutes in order to bring them in line with the current FIFA Standard Statutes, and organising elections accordingly by 30 June 2017 at the latest."
The worst case scenario could see Argentina's FIFA affiliation revoked, disqualifying them from 2018 World Cup qualification and preventing domestic sides taking part in international competition.
This will be a severe concern for Boca Juniors fans, who are scheduled to watch their team face Independiente del Valle in the Copa Libertadores semi-finals next month.
Domestic concerns are heightened by a lack of clarity over the structure of the upcoming season's league campaign.
Shortly before his death, Grondona authorised a change to the structure of Argentina's top flight that resulted in a 30-team tournament, running out of sync with Europe, for 2015.
After one season those teams were split into two groups for a transitional competition, but there is not yet clarification over how the 2016-17 season will be run.
With confusion and chaos paramount in all sections of Argentinian football, Messi's retirement may well have come even if he had got his hands on the trophy.