High investments and low economic efficiency of agricultural biogas plants operating on farms are two of the main barriers to the development of the biogas plant sector. Identification of economic and financial problems related to the operation of such facilities allows for the reduction of entry barriers for private investors, especially farmers. The aim of this research was to analyze the economic efficiency of investing in an agricultural biogas plant operating at a dairy farm. For the analysis, the case study method was applied. The economic efficiency of investment in a biogas plant was assessed using six different cash flow options. The NPV (net present value) and IRR (internal rate of return) methods were applied to assess the economic efficiency of the investment. It was found that the investment project for an agricultural biogas plant with a capacity of 0.499 MW located at a dairy farm required a subsidy of approximately 40–60% of the value of to ensure satisfactory economic efficiency. It has been shown that a particularly important aspect in assessing the economic efficiency of an investment in an agricultural biogas plant is the use of an economic calculation that takes into account the valuation and quantification of all positive external effects of such projects.