Bioenergy from energy crops is a source of negative emissions and carbon-neutral fuels in many 1.5/2 ∘C IPCC pathways. This may compete with other land uses. In contrast, ancillary biomass like by-products and waste is not primarily grown for energy and thus without land/food/feed competition. Here, we examine the availability and environmental impacts of ancillary bioenergy from agricultural sources under 190 circular agroecological strategies using the global food-system model SOLm for the year 2050. We find that there is a diverse option space for the future food and energy system to meet both global warming targets (1.5 ∘C) and food system sustainability (medium to highly organic) – a similar range of ancillary bioenergy global potential (55–65 EJ)from very different food systems (50%–75% organic agriculture and various levels of waste and concentrate feeding reduction). We find three trade-offs between food system sustainability and ancillary bioenergy provision. First, there is a clear trade-off between nutrient recycling and negative emissions potential. 1.4–2.6 GTCO2eq of negative emissions supplied through ancillary bioenergy with carbon capture and storage comes at the cost of nutrient deficits and resulting incompatibility with even a medium degree of organic farming. Second, reducing feed from croplands increases the ancillary bioenergy production with low shares of organic agriculture and reduces it for high shares. Third, food waste reduction reduces ancillary bioenergy provision. Hence, the sustainable transformation of the food system towards a less animal-based diet and waste reduction may conflict with a higher ancillary bioenergy provision, especially when the organic share is high as well. The policy implication of our results is that ancillary bioenergy can provide a similar range of future bioenergy as foreseen in IPCC AR6 illustrative pathways (±10% ) without additional land use or compromising food availability. However, higher ancillary bioenergy provision or additional negative emissions compete with food system sustainability; hence, we recommend policymakers consider aligning energy system planning with the compatibility of sustainable food systems simultaneously.