The loss of soil fertility across large parts of the world in recent decades gave an impulse to develop sustainable agricultural food production systems for the world's growing population. Organic agriculture is of particular interest in this respect, as manifested by 6.3 million hectares managed pursuant to EU Regulation 2092/91 in Europe. However, there is still need for scientific evidence that organic farming is really sustainable over the long term. Agricultural systems, in particular soils, are well buffered. Consequently, the adaptation of soil processes and soil-plant relationships from high-input to low external input farming may last decades. For instance, total soil carbon stocks normally respond slowly to changed farming practices. Similarly, the adaptation of soil fauna and flora to altered conditions usually occurs only after a prolonged period of time following conversion from high-input to low-input farming. Nutrient stocks in soils under conventional management are frequently high, and thus developments under reduced nutrient input have to be monitored. In low-input systems, crop yield as a measure of primary production is much more dependent upon fertile soils. Therefore, long-term trials are essential to assess the sustainability of farming systems and the underlying soil processes. There are in principle two approaches: The comparison of whole cropping systems or at least parts of them, or the comparison, as single factors, of farming practices inherent to a system, such as organic versus inorganic fertilization. We will present two of the oldest long-term trials in Europe dedicated to the question of agricultural sustainability in organic farming: The DOK farming system comparison in Switzerland, and the long-term fertilization trial in Darmstadt, Germany. In the DOK trial, the Swiss Federal Research Station for Agroecology (CH-Zurich) and the Institute of Organic Agriculture (CH-Frick) have been comparing organic and conventional farming systems in a crop rotation since 1978. The replicated field plot experiment was installed on a haplic luvisol on deep deposits of alluvial Loess. In 1980 a fertilization trial on a sandy orthic luvisol was started at the Institute for Biodynamic Research in Darmstadt, Germany. Under cultivation conditions of organic farming it comprises farmyard manure treatments with and without application of biodynamic preparations and inorganic fertilization. In both field trials the first experimental phase was focused on yield development, product quality and resource allocation. In the second phase the understanding of key soil processes and functions gained prominence. Several research groups are now working in the fields of soil microbial diversity, soil carbon transformation, phosphorus and nitrogen transformation, micronutrient status, soil-plant interface, soil food webs and food quality. Moreover, interactions between fertilization treatments and climatic parameters have been analysed. The experiments also serve as a unique basis for method development and evaluation and considerably facilitate interdisciplinary research work. The paper will highlight the importance of long-term experiments for the assessment of sustainability in organic farming with respect to soil fertility, resource use efficiency and yield.