Agriculture is one of the leading sectors on the global level contributing to greenhouse gas (GHG) emissions increase. With the utilization of biogas production technology within the agriculture sector, ecological benefits could be achieved, with immediate economic profit. Therefore, to retain economic profit and environmental sustainability, implementation of bioeconomy principles is of key importance. This paper examines four options of digestate treatment, which is identified as one of the highest operational cost for the biogas plant. A simple and robust model in Excel Solver was developed to determine the best solution for minimising GHG emissions and maximise profit for the biogas plant operator, through an upgrade of the plant with digestate treatment technologies. The model was implemented on a case of a Croatian biogas plant and the best solution in terms of GHG reduction and profit increase proved to be fertilizer production (Option 1), through a crystallization process of struvite within the digestate. This option obtains a significant reduction in GHG emissions compared to standard biogas production without additional upgrades (Option 4), by over 90%, and increase of profit for the biogas plant operator, which diversifies the income source and creates multiple positive impacts on the environment.