The article presents the evaluation of the economic efficiency of innovative projects as one of the significant stages of the strategic planning of innovative activities of the enterprise. The paper investigates the evaluation of economic efficiency and the strategic analysis of risks of the project to construct the biogas plant using the innovative technology «WiseSoil» for agricultural medium-sized enterprises. Hence, the authors have calculated the dynamic indicators of economic efficiency of the project, applied the method of real options to create the management flexibility for decision making under uncertainty and conducted Monte-Carlo simulation for the quantitative evaluation of risks of the innovative project. The results of the evaluation of the economic efficiency of the project to build the biogas plant with the innovative technology of processing of raw materials allow the authors to make a conclusion of profitable investments. The calculated dynamic indicators of economic efficiency determine the net present value of the innovative project, a payback period and an internal rate of return. Further, management flexibility in making strategic decisions for the project has been taken into account, namely, the application of the real option approach amounts to the evaluation of the call option to expand in connection with the putting into service the new reactor for the biogas plant. A quantitative risk analysis in the framework of strategic planning has shown a range of forecast values of NPV and the most probable and the threshold values of the NPV. The performed evaluation of the economic efficiency of the project will play a considerable role in the future planning and the development of innovation in the process of the elaboration of the strategic plan of innovative activities for medium-sized agro-enterprises.