It is not yet known if Allen will be replaced. Group chief executive Peter Marks has stated he is considering how to maintain "marketing momentum".
Allen joined the Co-op in 2004 and was behind the 2009 brand campaign featuring Bob Dylan's sixties hit, 'Blowin' in the Wind', to mark the completion of its corporate re-branding project. The £10m brand campaign highlighted its ethical and environmental credentials.
In January the Co-op group announced a company-wide restructure, made some of its marketing roles redundant and the unified the buying and marketing teams in its food business under a single leadership.
Debbie Robinson, director of food retail marketing and David Messom, director of food retail trading, both departed, with their positions ceasing to exist.
The group marketing department retained "a monitoring and governance role in ensuring universal brand standards are maintained across the whole group".
Allen became head of marketing at the United Co-operatives, in 2004 and was promoted to executive director of marketing for the Co-operative Group in 2007.
Prior to this Allen had stints as an accountant, financial analyst, lecturer in strategic management and marketing and also managing director at PA Consulting and Training.
Allen said: "I've had a fantastic six years with the Co-operative, during one of the most exciting periods of its history.
"I'm now looking to utilise the experience I’ve gained over that time and before joining the group, in a senior commercial management role."
Marks said: "I would like to thank Patrick for the contribution he has made to the Group over the past few years and wish him well as he now looks to develop his career further.
"Our brand has never been stronger or more relevant to our customers, members and the communities in which we operate.
"I shall, therefore, be considering the best way in which this marketing momentum can be maintained going forwards."
The Co-operative Group agreed to acquire Somerfield in 2008 for £1.57bn. The deal was completed in March 2009 and since then the group has been phasing Co-operative branded products into Somerfield stores. The harmonisation of the ranges should be complete by October.
In January Co-op rolled out a multi-million pound advertising campaign to mark the merger of the two supermarket businesses.
This attempted to illustrate how The Co-operative's acquisition of the Somerfield supermarket chain has enabled it to offer its best value deals, available across both stores.