In 2001, Protected Harvest was formally established as a 501(c)(3) nonprofit organization in Soquel, California.  Protected Harvest evolved out of a collaboration among World Wildlife Fund, the Wisconsin Potato and Vegetable Growers Association, and the University of Wisconsin. Over the course of five years, the collaboration resulted in a fresh market potato standard validated and certified by Protected Harvest. The standard was developed to include a unique, metric-based approach to measuring environmental and worker risk from pesticide active ingredients called the Pesticide Environmental Assessment System (PEAS).

Following the initial development phase in 2005, Protected Harvest worked with the Lodi Winegrape Commission to launch the Lodi Rules for Sustainable Winegrowing (LODI RULES) certification label. Three more specialty crop standards were launched in the following few years. A buyer-driven standard for citrus and stonefruit (Zeal) was launched with FreshSense in 2007.  A mushroom production standard was also launched in 2007 in partnership with Modern Farms Mushrooms.

A cut flower certification, BloomCheck®, was launched in partnership with the California Cut Flower Commission in 2015. BloomCheck® is California’s first sustainable cut flower certification program.

Protected Harvest continues to work with partners to grow existing certification programs. Protected Harvest is transitioning its validated certification standards from the use of the PEAS model to the Pesticide Risk Tool (PRT), the next generation of pesticide risk measurement. PRT will be integrated into various standards validated by Protected Harvest in the coming years.