Current organic agriculture performs well in several sustainability domains, like animal welfare, farm profitability and low pesticide use, but yields are commonly lower than in conventional farming. There is now a revitalized interest in increasing yields in organic agriculture to provide more organic food for a growing, more affluent population and reduce negative impacts per unit produced. However, past yield increases have been accompanied by several negative side-effects. Here, we review risks and opportunities related to a broad range of sustainability domains associated with increasing yields in organic agriculture in the Northern European context. We identify increased N input, weed, disease and pest control, improved livestock feeding, breeding for higher yields and reduced losses as the main measures for yield increases. We review the implications of their implementation for biodiversity, greenhouse gas emissions, nutrient losses, soil fertility, animal health and welfare, human nutrition and health and farm profitability. Our findings from this first-of-its-kind integrated analysis reveal which strategies for increasing yields are unlikely to produce negative side-effects and therefore should be a high priority, and which strategies need to be implemented with great attention to trade-offs. For example, increased N inputs in cropping carry many risks and few opportunities, whereas there are many risk-free opportunities for improved pest control through the management of ecosystem services. For most yield increasing strategies, both risks and opportunities arise, and the actual effect depends on management including active mitigation of side-effects. Our review shows that, to be a driving force for increased food system sustainability, organic agriculture may need to reconsider certain fundamental principles. Novel plant nutrient sources, including increased nutrient recycling in society, and in some cases mineral nitrogen fertilisers from renewable sources, and truly alternative animal production systems may need to be developed and accepted.