The scheme trains prisoners to work in its kitchens while earning an accredited City & Guilds NVQ.
The first Clink Restaurant opened to the public in 2009 at HMP Highdown in Sutton where it remains to this day.
The charity says the restaurant at Styal will close due to a number of factors including costs and participant numbers.
Donna-Marie Edmonds, Chief Executive of The Clink Charity, said: “The decision not to renew our contract at HMP Styal has been made with an incredibly heavy heart. The Clink Charity’s mission is to reduce re-offending and we have been doing this at Styal, producing outstanding results for over a decade.
“Although the restaurant will officially close this summer, our partnership at Styal will be remembered not only for its landmark training outcomes, but as a beacon of hope, where women have sought refuge and rehabilitation.”
As one of those students puts it: ‘If it wasn’t for my journey at The Clink, I wouldn’t be where I am now.’