The outspoken director will leave at the end of September following more than 20 years with the association, 15 as director.
"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," he said.
"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."
The association is now looking for a replacement for Holden. "Patrick's unique talents, experience and skills will be very difficult to replace," said Orna Ni-Chionna, the Soil Association's chair of trustees. "But we know that he will bring urgently needed impetus to the international initiatives he will be working on."
Sales of organic produce have plummeted in recent years as consumers rein in their spending, falling 12.2% to £1.3bn in the multiples last year, according to the Soil Association. However, it has predicted modest growth of 2% to 5% during 2010.