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The advent of the COVID-19 pandemic and the establishment of a new transitional government in Sudan with rejuvenated relations with the international community paved the way for external assistance to the EU COVID-19 response project, a project with a pioneering design within the region. The project sought to operationalize the humanitarian–development–peace nexus, perceiving the nexus as a continuum rather than sequential due to the protracted nature of emergencies in Sudan and their multiplicity and contextual complexity. It went further into enhancing peace through engaging with conflict and post-conflict-affected states and communities and empowering local actors. Learning from this experience, external assistance models to low- or middle-income countries (LMICs) should apply principles of flexibility and adaptability, while maintaining trust through transparency in exchange, to ensure sustainable and responsive action to domestic needs within changing contexts. Careful selection and diverse project team skills, early and continuous engagement with stakeholders, and robust planning, monitoring and evaluation processes were the project highlights. Yet, the challenges of political turmoil, changing Ministry of Health leadership, competing priorities and inactive coordination mechanisms had to be dealt with. While applying such an approach of a health system lens to health emergencies in LMICs is thought to be a success factor in this case, more robust technical guidance to the nexus implementation is crucial and can be best attained through encouraging further case reports analysing context-specific practices.