Bioenergy with carbon capture and storage (BECCS) is a key option for removing CO2 from the atmosphere over time to achieve climate mitigation. However, an overlooked impact of BECCS is the amount of nutrients required to sustain the production. Here, we use an observation-driven approach to estimate the future bioenergy biomass production for land-use scenarios maximizing BECCS and the pertaining nutrient requirements. The projected global biomass production during the 21st century is comparable to the CO2 removal target for 2 °C warming scenarios. However, 9–19% of this future production hinges on agrotechnology improvement, which remains uncertain. Additional nutrients from fertilizers, corresponding to 56.8 ± 6.1% of the present-day agricultural fertilizer, will be needed to replenish the nutrients removed in harvested biomass at the end of the century, resulting in additional costs and greenhouse gas emissions. Our study reveals the nutrient challenges associated with BECCS and calls for additional management efforts to grow bioenergy crops in a sustainable way.