Although no legal sustainability criteria have been formulated for electricity and heat production from biogas, the sustainability and profitability of large-scale biogas plants which use mainly energy crops is now questioned. Small (farm-size) biogas plants characterized by CHP electrical output in the range between 15 kWel and 99 kWel, operating on agricultural wastes and by-products, seem more suitable; however, the variety of feedstock may be crucial in the proper design and operation of such family biogas plants. This paper aims to present the problems that occurred in small agricultural biogas plants fed with sheep manure (SM), horse manure (HM), and grass-clover silage (GCS). This paper also focuses on analyzing the energy balance and carbon dioxide (CO2) emissions related to four technological solutions (Scenarios 1–4) based on various feedstocks, grinding and feeding systems, and wet/dry fermentation. The biogas plant was originally based on dry fermentation with an organic loading rate ~10.4 kgVS·m−3·d−1, a hydraulic retention time of 16 days, and temperature of 45 °C in the fermentation chamber. The material was shredded and mixed in a mixing device, then the mixture of manures and silage was introduced to the horizontal fermentation chamber through a system of screw feeders. The biogas and the digestate were collected in a reinforced concrete tank. The biogas was sent to the CHP unit of an installed electrical power of 37 kWel, used to produce electricity and recover the heat generated in this process. Scenario 1 is based on the design assumptions used for the biogas plant construction and start-up phase. Scenario 2 includes a new feeding and grinding system, in Scenario 3 the feedstock is limited to SM and HM and wet fermentation is introduced. In Scenario 4, a dry fermentation of SM, HM, and maize silage (MS) is assumed. Avoided CO2 emissions through electricity and heat production from biogas were the highest in the case of Scenarios 1 and 4 (262,764 kg CO2·y−1 and 240,992 kg CO2·y−1) due to high biogas production, and were the lowest in Scenario 3 (7,481,977 kg CO2·y−1) because of the low specific methane yield (SMY) of SM and HM. Nevertheless, in all scenarios, except Scenario 3, CO2 emissions from feedstock preparation and biogas plant operation are much lower than that which can be avoided by replacing the fossil fuel energy for the electricity and heat produced from biogas. Our observations show that a small agricultural biogas plant can be an effective energy source, and can contribute to reducing CO2 emissions only if the appropriate technological assumptions are adopted, and the entire installation is designed correctly.