There is ongoing debate among stakeholders about the future development of agricultural and food systems to meet the global challenges of food supply, biological and cultural diversity, climate change, and social justice. Among other options, agroecology and organic agriculture are discussed. Both have similar goals and use a systems approach; however, they are recognised and received differently by stakeholders. Here we review and compare principles and practices defined and described in EU organic agriculture regulations, International Federation of Organic Agricultural Movement (IFOAM) norms, and agroecology scientific literature. The main finding are as follows: (1) Regarding principles, EU organic regulations mainly focus on appropriate design and management of biological processes based on ecological systems, restriction of external inputs, and strict limitation of chemical inputs. IFOAM principles are very broad and more complete, and include a holistic and systemic vision of sustainability. Agroecology has a defined set of principles for the ecological management of agri-food systems, which also includes some socio-economic principles. (2) Many proposed cropping practices are similar for EU organic, IFOAM, and agroecology, e.g. soil tillage, soil fertility and fertilisation, crop and cultivar choice, crop rotation, as well as pest, disease and weed management. In contrast, the origin and quantity of products potentially used for soil fertilisation and pest, disease, and weed management are different. Additionally, some practices are only mentioned for one of the three sources. (3) In animal production, only a few proposed practices are similar for EU organic, IFOAM, and agroecology. These include integration of cropping and animal systems and breed choice. In contrast, practices for animal management, prevention methods in animal health, animal housing, animal welfare, animal nutrition, and veterinary management are defined or described differently. (4) Related to food systems, organic agriculture focusses on technical aspects, such as food processing, while in agroecology there is a prominent debate between a transformative and conformative agenda. Both agroecology and organic agriculture offer promising contributions for the future development of sustainable agricultural production and food systems, especially if their principles and practices converge to a transformative approach and that impedes the conventionalisation of agro-food systems.