The utilization of coproducts is a strategy that can be applied to increase the economic and environmental performance of industrial processes and thus reach an objective targeted in several environmental policies. In multi-output production processes, allocation needs to be performed to assess the products’ environmental and economic performance. It is crucial to choose an adequate allocation method, because this choice has been shown to strongly influence overall outcomes. Consequently, rash choices can lead to poor decision-making. Various ways to apply and combine allocation methods can be found in the academic literature, but it is often difficult to find sufficient guidance on how to choose an allocation method for a specific context. This study explores practitioners’ perceptions of the cost and environmental impact allocation methods used in biorefinery development (lignin, fiber fines) by applying the analytic hierarchy process (AHP). Results indicate that professional background represents a major factor influencing individual preferences and, thus, the selection of specific allocation methods. Policy makers should be aware that practitioners with different professional backgrounds have varying preferences for different allocation methods and that this influences the overall assessments. These factors, in turn, affect the interpretation of results, further decision-making and, ultimately, the realization of environmentally sound and economically viable biorefinery projects. This issue deserves more attention in biorefineries, but also in other multi-output production processes. The findings indicate a need to consider multidisciplinary, diverse views and knowledge when conducting such assessments and to display the underlying approaches transparently.