The European Parliament recently adopted a plan for a European strategy for the promotion of protein crops for food and feed. While the motivation is to reduce further deepening of the dependence on third-party imports, it is also anticipated that increased sourcing of protein feed from the EU will contribute to reduce deforestation and lower GHG emission footprint from EU livestock production. However, a significant part of the protein meals currently sourced from the EU is the result of a different policy, the Renewable Energy Directive, that promotes the use of vegetable oil for fossil fuel substitution in the EU transportation sector. This paper compares two different strategies to decrease reliance of the EU feed protein market to imports - direct support to oilseed production, and incorporation targets for biodiesel in transport. We assess GHG emission impacts of these scenarios using GLOBIOM, a partial equilibrium model of agriculture and land use, enriched with detailed representation of the oilseed supply chains. The results show that direct substitution of soybean feed with protein meal from rapeseed and sunflower decreases deforestation related GHG emissions even though increased demand for agricultural land contributes to higher GHG emissions from agricultural production. Direct substitution of soybean feed leads to net savings if the protein crops are sourced from Europe. However, when a demand for vegetable oil-based biofuel is introduced as the primary driver of feed substitution, the land-use emissions go in opposite direction, with net increase in overall GHG emissions, partly due to additional imports of palm oil from Southeast Asia. Therefore, a supply-oriented policy targeting domestic protein and oil crops appear environmentally preferable to sponsoring demand of vegetable oil for energy use, which shows the importance of connecting better the discussions on the Renewable Energy Directive and the European strategy for the promotion of protein crops for food and feed.