Local organic food supply chain partners face uncertainties such as poor collaboration, communication and information sharing that cannot be reduced through the application of traditional, quantitative supply chain design and management techniques. Such techniques are known to improve supply chain coordination and efficiency, but they do not adequately consider major aspects of local organic food supply chains such as ethics, sustainability and human values that influence decision making and thus, supply chain activities. Supply chain design and management approaches suitable to small-scale, local organic food enterprises are lacking and need to be developed. The aim of this paper is to suggest Soft Systems Methodology (SSM) as a new and suitable approach to design and manage local organic food supply chains. We illustrate how SSM can be used to reduce uncertainties within local organic food supply chains based on a German case study within the organic cereal sector. This illustration serves to identify benefits of using SSM compared with ad hoc, pragmatic and less structured approaches. Organisation of thought, intervention and change, as well as action-oriented, meaningful and participatory decision making are the major benefits. SSM is a promising alternative to traditional supply chain design and management techniques, and an approach to enable long term collaboration, coordination and communication along local organic food supply chains.