A federal judge in San Fransisco has approved a court settlement that commits the Environmental Protection Agency to fundamentally changing how it regulates pesticides, as well as a pilot program that will restrict pesticide use on millions of acres in Western Oregon and Western Washington to protect a rare butterfly.

U.S. District Court Magistrate Judge Joseph Spero signed the agreement Monday between the EPA and the Center for Biological Diversity and Pesticide Action Network.

The EPA agreed to drop its chemical-by-chemical, species-by-species approach to evaluating how pesticides affect federally protected species. Instead, the agency will develop separate “strategies” for herbicides, rodenticides, insecticides and fungicides.

The EPA said in a press release Tuesday that the agency’s traditional approach to fulfilling its obligations under the Endangered Species Act was too slow and exposed the agency to lawsuits.

“This agreement is a win-win-win to protect endangered species, ensure the availability of pesticides needed to grow food across America, and save considerable time and taxpayer expenses required to further litigate this case,” EPA assistant administrator for chemical safety Michal Freedhoff said in a statement.

The Center for Biological Diversity and Pesticide Action Network filed the lawsuit in 2011, alleging the EPA violated the ESA by approving 382 pesticide active ingredients.

The suit was narrowed to 35 active ingredients, but was still referred to by the EPA as the pesticide “megasuit.”

The court settlement locks the EPA into actions that won’t be vulnerable to “changing political winds,” Center for Biological Diversity environmental health legal director Jonathan Evans said in a statement.

The EPA announced in June a ”vulnerable species pilot project” to protect the Taylor’s checkerspot butterflies in Western Oregon and Western Washington and 26 other species across the U.S.

The pilot project will introduce new restrictions on pesticide use in parts of 29 states. The settlement commits the EPA to consider expanding the pilot project to other species.

The USDA and state departments of agriculture criticize the pilot project as unreasonable and impractical. In some cases, growers would have to get permission from the U.S. Fish and Wildlife three months before spraying.

The Washington State Department of Agriculture said that including the Taylor’s checkerspot butterfly in the pilot project contradicted the U.S. Fish and Wildlife’s position that habitat loss, not pesticides, was endangering the species.

Washington state already monitors how pesticides are affecting federally protected species, state Department of Agriculture policy adviser Kelly McLain said.

The department will wait to see details of the EPA pesticide strategies and whether the agency revises the proposed pilot project in response to concerns by the department and others about its scope, she said.

“I don’t think we know for sure whether the plan for the Taylor’s checkerspot butterfly will go forward as written,” McLain said.