The concept of agroecological transition revives debates on how to deal with complexity and uncertainty. While the adaptive approach and its “adjust along the way” principle have been adopted as a relevant general framework to deal with partially irreducible uncertainty, the different approaches to the definition and management of uncertainty are rarely explicitated. In this chapter we highlight the diversity of these stances through brief presentations of research work that is related to agroecology and sustainable development, and anchored in various disciplines (modelling, management sciences, economics, ecology). This gives us a first glimpse of the variety of concepts used to describe uncertainty, characterising nature and the different approaches to manage it. It shows also that these definitions of uncertainties, clearly derived from particular disciplines or school of thought, can be applied together in a more or less complementary way. Finally, we discuss how this explicitation of the diversity of approaches to uncertainty contributes to highlighting different ways of defining the agroecological transition itself – especially between determinist or more open-ended approaches–, and identifies interdisciplinary research issues.