The UNFCCC Paris Agreement sets a goal of limiting the global temperature increase to “well below 2°C” and to pursue “efforts to limit the temperature increase to 1.5°C”. Most emission pathways that are compatible with these goals are heavily reliant on negative emissions technologies (NETs), especially biomass energy with carbon capture and storage (BECCS), at a global scale to remove CO2 from the atmosphere. The use of negative emissions in climate mitigation introduces a complex variety of technologies whose desirability, effectiveness and viability remain highly uncertain. This paper explores six key policy and governance challenges associated with BECCS, suggesting ways in which research could address some of these challenges: (1) How does BECCS fit with carbon budgets? (2) How negative is BECCS? (3) Can BECCS be delivered at sufficient scale? (4) Can sufficient biomass be provided sustainably? (5) How does BECCS fit into the policy context? (6) How does BECCS fit with climate agreements? Consideration of these challenges highlights the importance of a whole systems approach to assessing the use of BECCS and its potential as a keystone technology to deliver negative emissions.