Intensified trade cooperation between the EU and MERCOSUR has become one of the priorities of the EU’s foreign trade policy in recent times. In response to the Russian Federation’s invasion of Ukraine and the energy crisis, the EU is seeking to diversify its imports and cooperate with Latin America, which is one of the richest regions in renewable resources and is considered to have the greatest potential for the production and export of green hydrogen. Therefore, it is in the interest of the EU to conclude a free trade agreement with the MERCOSUR. Environmental protection is a problematic area of the negotiations. Even though the agreement would facilitate bilateral trade and promote development in various areas, there are concerns that increased trade cooperation could lead to intensified deforestation of the Amazon rainforest and have an overall negative impact on the biodiversity of this region. The aim of this paper is to quantify and estimate through econometric modelling the impact that more intensive trade cooperation between the EU and MERCOSUR would have on the environment. Econometric modelling involves regression analysis between environmental and macroeconomic indicators, where the dependent variable represents environmental indicators such as deforestation rate, greenhouse gas emissions, and the independent variable consists of economic indicators reflecting mutual trade between the EU and MERCOSUR. The contribution of this paper is to provide recommendations that can be used in negotiations on the free trade agreement between the EU and MERCOSUR in the context of environmental protection and the fight against the climate crisis.