Investments in small and medium-sized anaerobic digestion facilities have the potential to boost biogas production in Greece and other EU countries. This study aimed to evaluate the economic feasibility of anaerobic digestion facilities equipped with combined heat and power (CHP) units ranging from 50 to 400 kW, while treating livestock waste. For this purpose, data were gathered from various livestock operations (dairy cattle, poultry, swine, dairy sheep and goats) regarding their annual production, revenues, electricity and fuel usage, and waste generation. Waste samples were then collected and analyzed to assess their biochemical methane production potential. The capital and operational costs of anaerobic digestion facilities, from 50 and 400 kW, were calculated using the equations developed within the “eMT cluster” project. Findings indicate that current feed-in tariffs (FITs) of 0.21 € kWh−1 are insufficient to incentivize investment in anaerobic digestion facilities with capacities below 250 kW, highlighting the need for increased FIT rates or capital expenditure subsidies. Recommendations include shifting towards simplified technology and business models with reduced farmer involvement, coupled with supportive legislative framework and long-term electricity price guarantees. These measures are expected to foster the implementation of anaerobic digestion projects in the animal husbandry sector.