Knowledge of differences between organic and conventional crop yields is of interest for farmers, advisors, politicians, and research scientists. Based on collected data from Danish organic and conventional mixed dairy farms the yield difference was estimated to be 21–37% in grain crops and 12–18% in fodder beets and grass/clover depending on climatic conditions and soil type. A method is presented to correct for the influence of year and geographic differences using crop and farm-specific simulated potential yields as regression variables in a linear statistical model. An interaction between potential yield and farming system indicates that other growth factors, possibly nutrients, are limiting the yields on organic farms more than on conventional farms. The results might facilitate modelling and evaluation of economics and energetics of organic farming at the crop and farm level.