"[6] In 2012 the company proposed to the Environmental Protection Agency (EPA) a $400 million upgrade to help move the refinery "closer to its processing capacity of 320,000 barrels of crude per day and also reduce emissions of nitrogen oxide and sulfur dioxide".

It was estimated that the refinery was responsible for 2% of Minnesota's total greenhouse-gas emissions, about 3.5 million tons of carbon dioxide per year.

By 2005 the refinery was "producing more gasoline, jet and other fuels while managing to cut harmful emissions into the air, water and ground by more than 50 percent since 1999", and took first place in the annual Minnesota Environmental Initiative awards that year.

"[10] The Pine Bend refinery also received four safety awards at the National Petrochemical and Refiners Association (NPRA) conference in 2001.

The refinery has been a MNSTAR-designated site since 2005, meaning that the Minnesota Department of Labor and Industry considers it a safe workplace with effective safety and health-management systems.

Another major exit route for distilled products is the Wisconsin Pipeline, which brings fuel eastward into the neighboring state.

Pine Bend Refinery dredges sediment from the nearby Mississippi River to ensure that its barges don't bottom out.