The future uncertainty and complexity of alternative socioeconomic and climatic scenarios challenge the model-based analysis of sustainable development. Obtaining robust insights requires a systematic processing of uncertainty and complexity not only in input assumptions, but also in the diversity of model structures that simulates the multisectoral dynamics of human and Earth system interactions. Here, we implement the global change scenarios, i.e., the Shared Socioeconomic Pathways and the Representative Concentration Pathways, in a feedback-rich, integrated assessment model of human-Earth system dynamics, called FeliX, to serve two aims: (1) to provide modellers with well-defined steps for the adoption of established scenarios in new integrated assessment models; (2) to explore the impacts of model uncertainty and its structural complexity on the projection of these scenarios for sustainable development. Our modelling shows internally consistent scenario storylines across sectors, yet with quantitatively different realisations of these scenarios compared to other integrated assessment models due to the new model’s structural complexity. The results highlight the importance of enumerating global change scenarios and their uncertainty exploration with a diversity of models of different input assumptions and structures to capture a wider variety of future possibilities and sustainability indicators.