The Association of Former Manchester United Players was founded in 1985 to support players who didn't make the huge salaries of those in the modern era.
United donated £40,000 each year to the not-for-profit, but The Sun says Ratcliffe has now moved to cut the club's contribution.
Trustee Jim Elms played for United's youth side and reserves and said: "We sent a letter to say we've not been paid. Nobody came out and told us so we had to send another letter.
"That's when we started hearing things that it was going to be the end of us."
Elms then spoke with United chief exec Omar Berrada and added: "It didn't go too well.
"Omar was non-committal. He's going to meet us again in January but he said he couldn't see it changing.
"He didn't seem to think that we were a necessity."