HMP Foston Hall in Derbyshire, a closed category prison, was awarded the trophy by the RHS.
Foston Hall governor Greg Riley-Smith said: "Winning Windlesham is a real accolade for both staff and prisoners at Foston Hall who have worked together to transform the environment into one which has a real positive influence on prisoner behaviour, so that we can demonstrate that the improved prison grounds have coincided with a marked drop in violence and incidents of self-harm.
He continued: "It is clear that the environment in which people live helps to mould their behaviour and where prisoners are able to work with staff to improve their environment the results are self-evident."
The trophy is made of an old Green Goddess Fire Engine bell and was devised in 1983 by Lord Windlesham, then chairman of the Parole Board.
It was designed to give prisoners a sense of worth and to encourage garden excellence.
RHS president Elizabeth Banks will make the presentation at a ceremony today, 18 August.
Twenty female prisoners look after the gardens, which include a conifer collection, two rock gardens and a range of glass houses.
The fruit trees, tomatoes, peppers, fennel and aubergines grown there are distributed to the outside world.
Horticulture now forms a key part of the resettlement agenda, offering inmates the chance to gain industry qualifications.
Participating prisoners are presented with a certificate acknowledging their assistance, signed by the RHS president.
Around 1,500 prisoners garden in prisons across the country and nearly thirty prisons took part in the 2010 Windlesham Trophy Competition.
Runner-ups, Bullingdon, Oxfordshire, have made their own collection of bee-hives to produce honey for local sales.
London’s Wandsworth prison took third place for their displays of vegetables in raised beds.
The fourth finalist, Dartmoor prison in Devon, grows vegetables for a scheme that distributes the produce to those unable to grow vegetables themselves.