With the RePowerEU plan the European Commission aims to boost biomethane production as part of its strategy for energy independence. Biomethane from manure is commonly considered as a circular solution that produces renewable energy, manages waste and reduces emissions. However, the intertwining of biomethane production with the livestock sector, one of the most impactful sectors in the EU and globally, is highly controversial, yet rarely discussed. In this Policy Perspective we argue how the reliance on manure as primary feedstock for biomethane is extending the EU's lock-in into unsustainable, business-as-usual livestock farming practices, replacing a natural gas dependency with an animal feed dependency from other continents, jeopardizing EU's strategic autonomy, while perpetuating neocolonial forms of extractivism. We highlight that such mechanisms are reinforced by blind spots in the Renewable Energy Directive emissions accounting standards which have overlooked the upstream impacts of biomethane production from manure, especially the ones in the Global South, obscuring the link between energy and food systems. These gaps contribute to rebound effects in indirect land use change and on-farm emissions, hindering environmental targets. Recommendations are provided to stimulate a critical discussion in which commonly held assumptions and narratives on biomethane production from manure are challenged.