Ted Kessler tweeted that Mr Heaton donated "a large sum" - which was shared among 40 members of staff - shortly after the magazine was closed.
He went on to say "it really was the most amazingly kind, selfless, generous act", adding "for some, it meant a bill could be paid".
The team commissioned the final ever Q award to present to the singer as a way of thanks.
Mr Heaton thanked the publication for their support over the years, wishing them all the best, after receiving the award on Friday.
The story was shared by Mr Kessler on the date the award ceremony was meant to have taken place.
He wrote: "We had the Roundhouse booked for two nights for the Q awards next week. We didn't have talent sorted when we had to COVID cancel in April, but Nadine Shah was presenting and the two gigs were Liam Gallagher one night, Paul Heaton & Jacqui Abbott the other.
"The only award we knew for sure was to Paul Heaton, as we'd heard he'd never won one."
He added: "Think of all the brilliant songs he's written for The Housemartins, Beautiful South, etc. Millions of records sold. No Q award (or Brit) for his song writing. So we knew he'd be Classic Songwriter.
"Then, a few days after Q closed, we got a message from him saying that to thank Q for all the support we'd given him over 35 years, he was going to donate a large sum to thank us in our turmoil. Obviously, I politely declined.
"He was insistent. I accepted the donation and shared it amongst over 40 staff and freelancers working for Q at the time, all of whose minds - like mine - were blown."
"We got him that award in the end. Britain's greatest living pop star. A true legend," Mr Kessler ended, sharing a picture of it.
After seeing Mr Heaton trending on Twitter, another user added: "I'm not sure if this is public knowledge yet, so apologies if I embarrass him, but ~10 years ago the transmitter died at our local community radio station, ALLFM and we couldn't afford to replace it. Paul quietly wrote a cheque."
After 34 years, the popular music magazine closed in July due to the impact of the coronavirus pandemic.