Abstract Organic farming (OF) is considered a promising solution for reducing environmental burdens related to intensive agricultural management practices. The question arises whether OF really reduces the environmental impacts once lower yields and all the changes in farming methods are taken into consideration. This question is addressed in a comprehensive study of Swiss arable cropping and forage production systems comparing OF to integrated production (IP) systems by means of the life cycle assessment (LCA) method. The LCA study investigated the environmental impacts of two long-term farming system experiments: the DOC experiment comparing bio-dynamic, bio-organic and conventional/integrated farming and the “Burgrain” experiment encompassing integrated intensive, integrated extensive and organic production. All treatments received similar amounts of farmyard manure. The system boundary encompasses the plant production system; storage and application of farmyard manure is included in the system boundary, the animal husbandry is not included. The Swiss Agricultural Life Cycle Assessment method (SALCA) was used to analyse the environmental impacts. In the overall assessment OF was revealed to be either superior or similar to IP in environmental terms. OF has its main strengths in better resource conservation, since the farming system relies mainly on farm-internal resources and limits the input of external auxiliary materials. This results in less fossil and mineral resources being consumed. Moreover the greatly restricted use of pesticides makes it possible to markedly reduce ecotoxicity potentials on the one hand, and to achieve a higher biodiversity potential on the other. This overall positive assessment is not valid for all organic products: some products such as potatoes had higher environmental burdens than their counterparts from IP. The main drawbacks identified for Swiss OF systems are lower yields. As a consequence some production factors are used less efficiently, thus partly negating the advantages of OF. Furthermore, the different manure management strategy leads to relatively high nutrient losses in relation to yield. These two points were shown to be the main priorities for the environmental optimisation of OF systems. The differences between the bio-organic and the bio-dynamic farming systems consisted in a slightly higher input of organic matter, a few applications of mineral fertilisers and copper applications in the former. The eco-efficiency analysis led to the conclusion that the optimisation of OF is mainly output-driven, i.e. that higher yields of good quality should be achieved with the available (limited) resources. On the contrary, optimisation of IP was found to be input-driven; the inputs should be used in a quantity and manner which minimise the environmental burdens per unit produced. The study showed that despite the efforts of recent years, there is still considerable room for the environmental optimisation of Swiss farming systems.