The aim of the paper is to give suggestions about how an agri-environment index can be designed by taking into account specific ecological and economical factors that reflect benefits and costs of biodiversity conservation. Main findings are that the general structure of an agri-environment index is recommended to be a benefits-to-cost ratio, whereby the conservation benefits are accounted for by the following factors which evaluate i) certain criteria that value the ecological quality of a site and point out its significance for biodiversity conservation (Conservation Significance Factor), ii) a criterion that reflects the connectivity of the site which is an important factor for species migration (Connectivity Factor) and iii) criteria that estimate the potential biodiversity outcomes induced by specific management actions (Conservation Management Factor). The Cost Factor reflects the amount of money that the landholder demands as compensation payment for his conservation services. The paper points out that an agri-environment index is a promising approach to encourage and compensate farmers for biodiversity-friendly management actions. Thereby, an improvement of the effectiveness and efficiency of European conservation payment schemes is a decisive contribution to biodiversity conservation in agricultural landscapes.