Interest in the anaerobic digestion (AD) of swine manures and slaughter waste continues to increase due to the potential to produce renewable energy in the form of biogas and due to the expanding market for carbon credits around the world. This paper provides an analysis of the anaerobic digestion types and operational schemes that are best suited to Croatian swine production. In addition, it proposes a methodology to optimize system selection and design by predicting biogas production quantity and quality based on the use of biochemical methane potential (BMP) assays followed by the use of pilot-scale reactors to make final system selections and estimate system hydraulic retention times (HRT) for the selected system design. A review of reactor configurations that are promising for swine manure and slaughter waste digestion suggests that a mesophilic, continuously fed AD system be investigated to digest a mix of Croatian large-scale swine manure and slaughter waste.