Since 1990, the Foundation for Deep Ecology has made more than 1500 grants to nonprofit organizations working to protect wilderness and wildlife, promote sustainable agriculture, and oppose pernicious forms of megatechnology. As of 2012, these funds totaled more than $52 million; FDE's overall philanthropy exceeds $73 million when costs related to the foundation's publishing program, grants associated with FDE books including for related educational campaigns, and other program work is added. In its early years, FDE granted under a fairly broad array of categories, but later in the 1990s its funding program was streamlined into three main program areas: Biodiversity and Wildness, Ecological Agriculture, and Globalization and Megatechnology.

Biodiversity and Wildness program grantees have included organizations that promote large-scale wilderness recovery including the Wildlands Project (now Wildlands Network), the Yellowstone to Yukon Conservation Initiative (Y2Y), and RESTORE: The Northwoods, as well as leading champions of endangered species such as the Center for Biological Diversity and Sea Shepherd Conservation Society. Ecological Agriculture grants have gone to pioneers in sustainable agriculture including The Land Institute, Occidental Arts and Ecology Center, and the Wild Farm Alliance. Globalization and Megatechnology program grantees include the International Society for Ecology and Culture, the Foundation on Economic Trends, and the International Center for Technology Assessment. A comprehensive list of the hundreds of nonprofits FDE supported during its first decade can be found in the report, “Foundation for Deep Ecology: The First Ten Years.”

Over the past decade, FDE’s grantmaking primarily focused on environmental campaigns in Chile and Argentina. The foundation’s primary program work in the United States has been its in-house publishing program. FDE does not accept unsolicited proposals for funding or book projects.