The artist has handed over the full amount of his £25,000 award cash to the MVT, which functions to preserve the UK's independent concert spaces.
He was given the award on October 16 as his latest record People Watching was chosen as the top album of the past year.
He has chosen to donate the funds to the MVT, in appreciation of the essential function local spots played in his early career.
"As an artist wouldn't be doing this success if it wasn't for all the shows I played around the region, and beyond, when I was starting out," said the artist. "These locations are legendary, but they are struggling."
From early 2023 onward, over 150 of these spaces have ceased operations – approximately 16 percent of the entire UK sector.
Over the past year, major artists including Pulp, Coldplay, the singer Katy Perry and Ed Sheeran have all backed the MVT in its attempts to keep the scene afloat, by adding a minor surcharge to their admission fees, which goes to help independent venues.
Fender also took part, raising more than £100,000 on his 2024 arena tour to support thirty-eight local spots across Britain.
These funds supported locations that were dealing with possible closure due to challenges caused by flooding, fires and personal losses, as well as permit problems, legal disputes and noise complaints.
Additional spaces received funding support in modernizing facilities and sound and lighting systems that directly benefitted performers and concertgoers.
"The idea that money from concerts in large arenas helps the independent spots, where it kicks off for musicians like me, is just logical," Fender has stated.
He is among several artists to donate his Mercury Prize prize money to good deeds.
In the band received the award in the year 1996 for their release the album, vocalist Jarvis Cocker announced that the group would give their cash to the non-profit the charity.
That year, rapper and singer Ms Dynamite split her award across a few organizations, such as the NSPCC and a Sickle Cell organization.
"I also gave a thousand pounds to Highgate Newtown, to their classes, because I practiced gymnastics when I was a child and they needed new equipment," she shared with a publication.
In recent years, Ezra Collective gave their funds to the youth organization that nurtured their group, in addition to other independent music bodies.
Also winners that year the group contributed their award to a MS organization after a friend was found to have the illness.
"Receiving the award was quite enough," stated singer Heather Small. "The cash was the cherry on top but we didn't need the extra, because we had the honor. So our success touched the lives of others."
In the past week, the Music Venues Trust shared it had saved several small stages in the South East, by transferring them to local control.
One venue in Southampton and The Croft in the city were acquired under the public acquisition scheme, which is backed by Arts Council England and music fans who purchase "ownership units" in the buildings.