It had also surrendered its Mangatangi coal mining permit, divested nearly 50% of land acquired for coal mining and would no longer mine coal.
The new moves were part of the pathway Fonterra mapped out with the Government last year to achieve net zero emissions across its manufacturing sites by 2050.
In a statement, chief operating officer global operations Robert Spurway said the co-operative's targets were ambitious and its commitment to meeting them was resolute because there was ''no alternative with climate change''.
''With 30 manufacturing sites across the country, the challenge ahead of us is clear but we understand the importance of getting on with it to help the country meet its international (climate change) obligations.''
By the end of the year, Fonterra would have divested a total of 206ha of land that had been acquired for coal mining.
The Stirling factory, which opened in 1983, was built by the Otago Cheese Company, formed after three small South Otago dairy companies merged. In 2010, Fonterra spent $7.75million upgrading the factory.