In 2012, Bunge came under criticism from NGO Survival International for sourcing its sugarcane from the ancestral land of the Guaraní people in Brazil. It has been reported by the tribe that crop production has brought pesticides and machinery that has damaged their health, as well as restricting them to a small area that has prevented them from hunting and practicing their traditions. Opposition from the tribe led to the killing of their chief Marcus Vernon by ranchers in January 2003. Survival requested Bunge to follow the example of the company Raízen, which agreed to stop the sourcing of sugarcane from the area in 2012.

In 2006, the United States Environmental Protection Agency filed charges against Bunge company regarding pollution emissions. This involved twelve soybean processing plants and corn mills in eight states throughout the US. Bunge was required to implement engineering changes and pollution control projects, estimated to cost $12 million, to reduce emissions at the facilities by 2,200 tons a year. The settlement also called for Bunge to pay a cash penalty of $625,000 and to spend $1.25 million to fund community-based environmental projects selected by and to be supervised by the impacted states. The state of Kansas will receive $22,000 of the $625,000 civil penalty, this being issued by the Kansas Department of Health and Environment.

Bunge sources about half of its palm oil from Sarawak Oil Palms. This company is clearing and draining globally-significant high conservation value peat forests for oil palm plantations, releasing vast quantities of greenhouse gas emissions. The company also cleared part of a proposed national park that was listed by the Malaysian government as a conservation area for threatened trees. The company is in conflict with local communities which claim native customary rights over areas where it operates. SOP has in the past worked with other Sarawak producers to undermine enforcement of Wilmar's No Deforestation policy, contributing to Sarawak status as the epicenter of peatland clearance in the world. The state cleared an incredible one-third of its peatlands between 2005 and 2010 alone, with SOP at the center of these activities.

Bunge has, however, engaged with civil society to facilitate conversations with SOP and other palm oil growers to address these issues. It has also expressed openness to addressing deforestation in other parts of Bunge’s operations such as soy in Latin America. The company reports that it will issue a sourcing policy by the end of 2014 that will address issues such as high carbon stock and high conservation value forests. However, the company has not yet provided any details.