During the last decade, the issue of major concern for the process industry is the reconversion of conventional chemical processes into more sustainable ones, especially in the light of the emission goals set by the EU for 2050. For this purpose several technologies exploiting cogeneration, biomasses and energy integration have been recently conceived. However, these strategies usually imply a reduction in terms of degrees of freedom and a higher sensitivity of the process to eventual uncertainties. In this case, external perturbations could compromise the profitability and sustainability of the system and the design based on nominal operating conditions is not sufficient anymore to assess the actual performance of the plant. In this research work the challenge concerning negative emissions plants and their performances under perturbed conditions is discussed in detail in order to outline and provide a quantitative methodology to enable a more conscious decision since the early design stage.