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Development assistance is a major source of financing for health in least developed countries. However, persistent aid fragmentation has led to inefficiencies and health inequities and constrained progress towards Universal Health Coverage (UHC). Malawi is a case study for this global challenge, with 55% of total health expenditure funded by donors and fragmentation across 166 financing sources and 265 implementing partners. This often leads to poor coordination and misalignment between government priorities and donor projects. To address these challenges, the Malawi Ministry of Health (MoH) has developed and implemented an architecture of aid coordination tools and processes. Using a case study approach, we documented the iterative development, implementation and institutionalization of these tools, which was led by the MoH with technical assistance from the Clinton Health Access Initiative. We reviewed the grey literature, including relevant policy documents, planning tools and databases of government/partner funding commitments, and drew upon the authors' experiences in designing, implementing and scaling up these tools. Overall, the iterative use and revision of these tools by the Government of Malawi across the national and subnational levels, including integration with the government's public financial management system, was critical to successful uptake. The tools are used to inform government and partner resource allocation decisions, assess financing and gaps for national and district plans and inform donor grant applications. As Malawi has launched the Health Sector Strategic Plan 2023–2030, these tools are being adapted for the 'One Plan, One Budget and One Report' approach. However, while the tools are an incremental mechanism to strengthen aid alignment, success has been constrained by the larger context of power imbalances and misaligned incentives between the donor community and the Government of Malawi. Reform of the aid architecture is therefore critical to ensure that these tools achieve maximum impact in Malawi's journey towards UHC. [ABSTRACT FROM AUTHOR]