Reactive nitrogen (N) flows (all forms of N except N-2) are greatly increasing worldwide. This is mainly due to the ever larger use of inorganic N fertilizers used to sustain the growing food production. N flows have major impacts on water, air and soil quality as well as on biodiversity and human health. Reconciling the objectives of feeding the world and preserving the environment is a great challenge for agriculture. One of the main ways to increase food production while reducing its detrimental effects is to increase the efficiency of N use. N use efficiency (NUE) is a commonly used indicator to estimate efficiency of N use at the farm scale, It is defined as the ratio of farm N outputs to N inputs. However, it has some inconsistencies and biases, which raises questions about its reliability for assessing N efficiency of farming systems, As a consequence, we propose a new indicator, called system nitrogen efficiency (SyNE), which is based on NUE and improves upon it in several ways. First, life cycle inventory references are used to estimate N emissions linked to the production of inputs outside the farm. Second, net N flows are calculated by subtracting inputs and outputs of the same product in the farming system. Third, manure is not considered an end product, unlike crop and animal products. Finally, the annual change in N in soil organic matter is estimated. SyNE therefore expresses the efficiency of a farming system in transforming N inputs into desired agricultural products. It takes into account all sources of N, including the annual change in soil N stock as well as N losses occurring during the production and transport of inputs. To test the relevance of this new indicator, 38 mixed farms were surveyed in Brittany, France, and their NUE and SyNE were calculated and compared. Sensitivity analysis was performed to estimate the contribution of each variable to both indicators. We demonstrate SyNE is a useful indicator for comparing the N efficiency of different farming systems. We discuss its use in combination with system N balance (SyNB), a N loss indicator at the system scale. The combination of both indicators gives a more reliable estimate of the productive efficiency and potential environmental impacts of N in various farming systems.