Browning is chair of the Food Ethics Council and has been a member of the Curry Commission on the Future of Farming and Food; the Agriculture and Environment Biotechnology Commission; and the Meat and Livestock Commission. She was awarded an OBE in 1998 for services to organic farming.
She runs a tenanted 1,350 acre organic livestock and arable farm in Wiltshire, which supplies organic meat to multiple retailers.
Her business recently diversified to take on the running of the village pub, successfully adding a restaurant.
Soil Association chair, Orna Ni-Chionna said: "We are delighted that Helen is to rejoin us as director. She is one of the true pioneers of the organic movement, and she has a unique breadth of practical experience as well as being an inspirational campaigner.
"It will be a privilege to have her back with us and to work with her closely in her new role."
Browning added: "Leading the Soil Association is a compelling, exciting and important challenge. No other role would have drawn me from the National Trust.
"But it is crucial to reconcile food production with care for the health and vitality of people, wildlife, farm animals and our countryside, and the Soil Association is the best placed organisation to provide much-needed practical solutions."
"I look forward to continuing the momentum of the last 65 years, and with the support of our members, farmers and growers, Council and staff, to take the Association into a new era."
Holden stood down from leading the Soil Association in September this year after 15 years in the role. Browning will take up the new post in early spring.