Holden will hand the reins over to his successor on September 30 following a publicly advertised recruitment process for the director role.
The move marks the end of an era as Holdren has been director of the Soil Association since 1995.
Patrick Holden, commenting on his decision to step down, said: "After 15 years as director and more than 20 years working for the Association I believe that now is the right time to hand over to a successor to take the work of the Association forward. Taking this step will free me from the demands of running an organisation and enable me to concentrate on promoting sustainable farming internationally. It has been an enormous privilege to serve the Soil Association over a period where interest in organic and sustainable food enjoyed tremendous growth and I should like to pay tribute to all those who have made my job so stimulating and rewarding over the years."
He added: "The Soil Association is in my DNA and I will remain deeply committed to the organisation and its philosophy and principles for the rest of my life. It is because of the importance of these issues and against the background of growing concern about the security and fragility of our food systems that I wish to give more time to work on an international level to accelerate the transition towards more sustainable food systems. I see this work as being closely aligned to the ongoing work of the Association, which I will continue to strongly support."
Soil Association chair of Trustees, Orna Ni-Chionna said: "Patrick is a leader of exceptional insight and wisdom. His unique talents, experience and skills will be very difficult to replace. But we know that he will bring urgently needed impetus to international initiatives and we are delighted that we will still have opportunities to work closely together."