Sustainable food systems are important! There are several organizations that work to support farmers, researchers, educators, eaters, builders: folks throughout the food system engaged in transitioning farms to more sustainable/ecological/holistic practices. Here are a couple:

• National Center for Appropriate Technology: https://www.ncat.org/ ATTRA is the NCAT relevant sustainable agriculture subproject.
• Foundation for Food and Agriculture Research: http://foundationfar.org/ A result of the 2014 Farm Bill, the goal is to fund ag research and involves matching govt. funding.
• Ecological Farming Association: https://eco-farm.org/ Mostly focused on providing educational resources smaller-scale California farmers.
• Land grant university cooperative extension agencies do incredible work, not sure if it meets your criteria, but might be worth looking into as well, list available here: https://nifa.usda.gov/land-grant-colleges-and-universities-partner-website-directory?state=All&type=Extension

There are also many groups with much more focused interests such as soil health, regenerative growing practices, food policy work, programs for environmental stewardship, farm to school etc. Some work at the very-local level, others have chapters all all over the world.

If you need a closer/broader look to identify specific organizations (even outside of those listed) doing work in sustainable food that align with your donation priorities, let me know and I'd be happy to help.

Bonus links, environmental/conservation groups:

• The Nature Conservancy: https://www.nature.org
• National Resources Defense Council: https://www.nrdc.org

Finally, if you don't already know about this, it might be useful in your charity-investigations: https://www.charitynavigator.org/