In 1999 a group of sustainable agriculture funders began meeting to discuss the various problems related to agriculture and food systems in California and the solutions available to address these areas of concern. From the beginning, the group had the vision to develop and implement a plan for a public policy and research agenda that supports the wholesale transition to a sustainable, regional food systems in California.

The funders decided to organize themselves as a work group, naming themselves the Funders Agriculture Working Group. They began educating themselves and each other with facts and data on the state of agriculture in California. They quickly discovered that there was no single, dependable source for information on the environmental and health effects of conventional agriculture. They also discovered that only a very small amount of private funding in the state went to sustainable food systems, and an even smaller amount of public and University dollars.

Because of the lack of comprehensive general information on the impact of agriculture and food systems on the state, the group decided to prepare a report describing the multiple problems with the current agricultural system and some of the solutions. The group began researching and conducting interviews with over 80 stakeholders for the new report, Roots of Change. After over a year of research and compilation, the group released the report to foundations and stakeholders in March 2001.

In the center of the Roots of Change report was the “Blueprint for the Transition to Sustainable Agriculture.” This document identified several of the key goals and objectives that must be achieved in order to launch the transition to sustainable food systems in the state.

In June 2001, the group met with stakeholders at two listening sessions to receive feedback on the "Blueprint for the Transition" included in the report and refine it with hopes of developing it into an agenda for research and policy change in California. To continue this process, FAWG held a meeting to bring together funders with public interest colleagues in July 2001. At this meeting, the two groups worked together to craft the top goals and actions for the movement.

Group members have given speeches and presentations to funders and activists at several conferences:

October 1999: Environmental Grantmakers Association Retreat, Asilomar
Winter 2001: Funders Concerned with Sprawl, Center for Ecoliteracy
Spring 2001: Kellogg Conference on Sustainable Agriculture, Pittsburgh
April 2002: Kellogg Food and Society Conference, Denver
June 2002: Federal EPA Agriculture Annual meeting, San Francisco
October 2002: Bioneers Conference, San Rafael
February 2003: Family Foundation Conference, San Jose

In addition, the group held a variety of events to educate funders:

May 2001, Roots of Change Symposium, the group conducted a symposium to release the landmark report, Roots of Change. A panel of experts gave various views from the field, the newsroom, and the laboratory. Speakers included: Arlie Schardt, Environmental Media Services; Margaret Mellon, Union of Concerned Scientists; Bob Scowcroft, Organic Farming and Research Foundation; Craig McNamara, McNamara Farms.
August 2001, Farm tour, the group completed a guided tour of local farms, from conventional to organic.
Sept 2001, Inaugural Quarterly Meeting, the group held its first quarterly meeting to educate and engage other funders. Speakers included Jim Tischer and Judith Redmond from the Community Alliance with Family Farmers and Mike Sutton from the Conservation Program at the David and Lucile Packard Foundation.
January 2002, Winter Quarterly Meeting, the group held its second quarterly meeting in San Francisco, California. Speakers included Mario Gutierrez from the Cross-cutting initiatives program at California Endowment and Andrew Kimbrell from the Center for Food Safety.
April 2002, Spring Quarterly Meeting, the group held its third quarterly meeting in Los Angeles, California. Speakers included Gene Bauston from Farm Sanctuary; Robert Gottlieb from the Urban Policy , Occidental College, Larry Yee, Director of the UC Extension Office, Ventura County; and Phil McGrath of McGrath Family Farms.
June 2002, Summer Quarterly Meeting, the group held its fourth quarterly meeting in Sausalito, California. Speakers included Sean Swezey from the University of California Sustainable Agriculture Research and Education Program and Claire Cummings from KPFA radio 94.1, where she hosts a weekly show on food and farming.
January 2003, Convened the first meeting of the Roots of Change Council at the launch of the ROC Fund; this meeting included funders and the ROC Council members. 
April 2003, Presented at the COF Family Foundations Conference at a session on creating foundation collaboratives and finding opportunities for collaboration.
May 2003, Co-hosted a Quarterly meeting with the California Rural Funders Group. Held at the Sierra Health Foundation, the meeting attracted over 40 funders and included an overview of the state of food systems in California and a report on the successes of sustainable alternatives in Marin County.
September 2003, Fall Food Systems Tour of Marin County, exploring alternative food systems in Marin and the role of county government in promoting sustainability.
December 2003, FSFS session on funding policy work at the Sustainable Agriculture and Food Systems Funders annual forum.
May 2004, Organized two brown bag discussions in May for FSFS members on EPA regulations as they pertain to food systems issues. The second brown bag, focused on GMO issues, led to the creation of an education program planning team to develop events later in the year on GMO issues.

In summer 2002, the group decided to change its name to the Funders for Sustainable Food Systems. The group decided on this change because through research and discussion, members identified that the roots of the problem were innately linked not only to agriculture, but to many sectors of the food system, including fisheries, food security, nutrition issues, labor rights, and more.