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The article presents the results of magnetic and ground‐penetrating radar (GPR) research carried out in Old Dongola in northern Sudan in 2018 and 2020, within the framework of a project designed to investigate the transition from Christianity to Islam taking place in the capital of the Nubian kingdom of Makuria. The integrated datasets from the application of two geophysical methods, of which one is the standard magnetic method used on sites in the Nile Valley and the other ground‐penetrating radar, enhanced the archaeological interpretation, focused in this case on a reconstruction of the urban layout of the 16th–18th‐century Funj settlement within the walls of the Dongola Citadel. The magnetic method, the effectiveness of which has gone unquestioned with regard to the study of silt architecture in the Nile valley, was successful in mapping the general outline of the settlement on the Citadel hill and in the quarter north of the walls. The GPR survey (450‐MHz antenna) provided a much more detailed image of the street grid and was much more effective than the magnetic method in tracing the course of mud‐brick walls in a sandy matrix containing baked brick rubble. Verification of the geophysical results through the excavation of selected parts of the Citadel not only satisfied the objectives of the archaeological project, which was to establish the overall street and building layout in the research area, but also confirmed the effectiveness of the two prospection methods applied in combination and the potential of integrated research with the use of the GPR and magnetic methods for the study of mud‐brick and baked brick architecture on settlement sites in Sudan. [ABSTRACT FROM AUTHOR]