State transitions of ecosystems have received wide attention, in particular in the context of catastrophic shifts. This special issue focuses on observational, experimental, and theoretical studies elucidating processes as they occur during state transitions providing insights into feedback controls and threshold like behaviors of ecosystems. Particularly, processes contributing to self-organized pattern formation of young ecosystems in the very early stage of development are discussed in this issue. In comparison to the high complexity of mature natural systems, the initial developmental stage of ecosystems is less complex and less interlinked. Therefore, the analysis of young ecosystems in their initial developmental stages or ecosystems that have undergone severe disturbance may pave the way in disentangling the complex process web and might be helpful to better understand the functioning of the ecosystem. In this regard, the contributions to this special issue deal with the following questions: (i) what are the most relevant structures and processes contributing to a state transition in particular for the very initial phase of an ecosystem, (ii) what are possible feedback controls between the evolving structural elements, (iii) can different phases of initial ecosystem development be distinguished, (iv) and what are the differences between the functioning of initial systems compared to established ecosystems. Within this context results obtained in the artificially constructed watershed Chicken Creek (Germany) are presented. Additional submissions focusing on heavily disturbed landscapes caused by natural disasters or by anthropogenic activities are most welcome.