Improving nitrogen (N) efficiency is a priority for increasing food production while reducing its environmental impacts. N efficiency indicators are needed to achieve this goal, but current indicators have some limitations. In particular, current N efficiency indicators are not appropriate tools to compare farming systems with different types of production because animal N efficiency is, by nature, lower than crop N efficiency. A novel N efficiency indicator called “relative N efficiency” was developed to address this issue. It was calculated as the ratio of the actual N efficiency of the farming system to the weighted mean of the potential efficiency of each type of product output provided in literature reviews. Relative N efficiency was calculated for 557 farms of various types from France and Italy. The relative N efficiency indicator was validated by comparison with a statistical approach based on multiple linear regression. Statistical analysis showed that relative N efficiency was independent of production type and could therefore be used for unbiased comparison of different farming systems. Relative N efficiency was particularly interesting when comparing mixed farming systems with different proportions of animal and crop production.