Lately, the model of circular economy has gained worldwide interest. Within its concept, waste is viewed as a beneficial resource that needs to be re-introduced in the supply chains, which also requires the use of raw materials, energy, and water to be minimized. Undeniably, a strong link exists between the bioeconomy, circular economy, bioproducts, and bioenergy. In this light, in order to promote a circular economy, a range of alternative options and technologies for biowaste exploitation are currently available. In this paper, we propose a generic methodological scheme for the development of small, medium, or large-scale units of alternative biowaste treatment, with an emphasis on the production of bioenergy and other bioproducts. With the use of multi-criteria decision analysis, the model simultaneously considers environmental, economic, and social criteria to support robust decision-making. In order to validate the methodology, the latter was demonstrated in a real-world case study for the development of a facility in the region of Serres, Greece. Based on the proposed methodological scheme, the optimal location of the facility was selected, based on its excellent assessment in criteria related to environmental performance, financial considerations, and local acceptance. Moreover, anaerobic digestion of agricultural residues, together with farming and livestock wastes, was recommended in order to produce bioenergy and bioproducts.