The European Innovation Partnership in Agriculture (EIP-AGRI) was initiated by the European Commission for social benefits and the modernization of the overall economy through innovation. Better and faster results are expectingby fostering collaboration between scientists, agricultural advisors and farmers. The main problem is how to evaluate the effectiveness of innovation partnership projects in agriculture, with what indicators to define and measure it? To address this problem, a methodology for evaluating the effectiveness of innovation partnerships in agriculture hasneeded. This article presents the methodology of evaluation of the effectiveness of innovation partnership in agriculture, which details the selected evaluation indicators, determines their significance, and provides guidelines for the interpretation of the results of efficiency evaluation. The developed evaluation methodology has tested using the project data of EIP groups operating in Lithuania. The methodology for evaluating the effectiveness of innovation partnerships in agriculture is relevant fromboth a scientific and practical point of view.