During the last two decades, organic agriculture has been considered superior to conventional production in many respects. In particular, environmental, energy consumption aspects, and food quality have been in focus. The basis for organic practices is derived from philosophies about nature and not natural sciences. Ecological processes and cycles are proposed to serve as a model providing guidelines for how to manage nature. However, the purpose of agriculture is not to emulate ecological processes, but to use and manage natural resources for the purpose of food production. A deeper and scientifically based analysis of long-term organic field experiments revealed that organic yields are lower than conventional ones. The primary cause for lower yields in organic systems is N shortage. Neither nutrient-use-efficiency, nor N leaching is improved through organic methods. Leaching of N per area is often similar between organic and conventional systems but expressed in relation to yield, leaching is considerably lower in conventional production. Due to lower organic yields, the input of crop residues to soil is lower. Thus, organic agriculture is not an option to sequester more carbon in soils than conventional systems. The argument by the organic movement to grow legumes instead of using inorganic N fertilizer, in order to save energy, cannot be concluded from a comparative energy analysis. Although use of N fertilizer is the largest post in the energy budget of conventional farming, it is also true that correct use of nitrogen fertilizer gives a high positive net energy balance whereby the energy output is 7-fold higher than the energy required for N fertilizer production. In summary, it remains to be further discussed whether organic agricultural methods are a sound contribution, as organic principles exclude other potentially superior solutions.