Agricultural crop residues represent a significant part of the biomass potentially available for renewable energy systems. Sustaining soil organic carbon (C) is a common limiting factor applied to the biophysically available resource to determine crop residues potential for bioenergy. Studies quantifying this potential have so far largely considered crop biomass to produce renewable energy as being independent from the energy conversion pathway. However, the conversion method has great influence on how much C in crop residues can be returned back and retained in soils. Here, we applied the C-TOOL soil C model for two extreme conversion pathways of agricultural straw management in terms of C returned back to soils, using Denmark as a case study. Those were anaerobic digestion, involving the return of recalcitrant C to fields, and combustion, involving no C returns to agricultural fields. Danish agriculture was represented by six different soil-cropping schemes units on which our two extreme bioenergy pathways were modelled. We applied a premise that for a given geographical unit, the same long-term soil C level needs to be achieved under these extreme bioenergy scenarios; therefore, we identified how much straw could be removed from agricultural fields in each case while maintaining equal soil organic carbon (SOC) levels. We found that at the scale of the whole country, only 26% of the straw potential can be harvested for use in combustion to maintain in average long-term SOC at the same level as it would have been with the anaerobic digestion scenario. Thus, consideration for the biomass conversion pathway is important when identifying agricultural residue potentials for energy conversion while ensuring that SOC level is not compromised.