Nick Francona’s tenure as the Mets’ assistant director of player development ended in recent weeks amid controversy over his criticism of Major League Baseball’s non-transparency regarding proceeds from military-themed apparel worn by players on Memorial Day.

The son of Indians manager Terry Francona was fired by the Mets, who he claims acted “cowardly” in caving to MLB, which he had challenged with public denouncements regarding the military apparel issue. The apparel is sold as MLB-licensed merchandise.

The 33-year-old Francona, a US Marine who commanded a scout-sniper platoon in Afghanistan, now believes his baseball career is finished. Francona was previously fired by the Dodgers after a clash with Gabe Kapler, then the organization’s director of player development. Francona alleged Kapler, now the Phillies manager, discriminated against him after he sought help from an organization that treats veterans for “invisible wounds of war.” The Dodgers denied the allegations and MLB officials investigated the matter, but determined no action was warranted against Kapler.

“I don’t feel like I am the morality police and tell people how to observe Memorial Day properly,” Francona said Monday in a phone interview with The Post. “Major League Baseball has proactively waded into these waters and I think [criticism] is fair when you are going to sell apparel. They are explicitly marketing this as Memorial Day and tying it to the memory of dead soldiers.”

Francona said he repeatedly asked MLB for evidence the proceeds from the Memorial Day apparel were directed toward charities connected with military families, but was stonewalled each time. He then began raising the issue on Twitter.

In late May he was informed by Mets general manager Sandy Alderson — who has since taken a medical leave of absence from the club as he battles recurring cancer — the Mets had decided to fire him. Francona, who arrived to the organization in spring 2017, said he was told his work performance wasn’t the issue, but his stand on the military apparel proceeds had forced his dismissal.

Alderson, a former Marine who served in Vietnam, did not return a message seeking comment, but Francona produced an email exchange between the two in which the GM warned Francona he was beginning to “undermine” the Mets’ military and veterans agenda.

“I felt like [the Mets’] actions in this were a little cowardly,” Francona said. “When it came time to do the right thing they crumbled under pressure and chose convenience and I think the pressure from the Commissioner’s Office and other teams, expediency was the preferred course for them. I don’t think that is a surprise to anyone. That is kind of how they operate.”

A spokesman for the Commissioner’s Office, in an email to The Post, said there is “absolutely no truth” to the allegation MLB applied pressure on the Mets to dismiss Francona.

The Mets issued a statement to The Post: “Nick Francona is no longer a member of the organization. We wish him the best in his future endeavors.”

Francona said he was more “disappointed” than “angry” with the Mets for their decision to fire him. The Wharton School of Business at Penn graduate has attacked the organization on Twitter and painted a level of dysfunction within the organization he said was not surprising given his preconceived notions about working for the Mets.

“There was something liberating about the fact actually that you know there are some limitations when you come to the Mets so this isn’t an ideal organization and a highly functioning place,” Francona said. “But do the best you can with that in mind. That is like a fun challenge to embrace and something I actually enjoyed.”

Francona said he was told by team COO Jeff Wilpon that he was making a “big impact” with his initiatives within the farm system. The fact Wilpon left Francona’s firing to Alderson bothered Francona.

“You would like somebody like that to step up and have the courage to tell it to you straight and not hide behind it,” Francona said. “That is kind of a general theme there, where [Wilpon’s] presence, whether direct or not, is kind of always in the background, hovering over stuff and sometimes it’s not even real and it has an impact, which is going to make things hard.”