A universal challenge in methodology used to study the ecology, conservation and evolutionary biology of migratory species is the quantification of connectivity among breeding, wintering and stopover sites. For the avian Eurasian-Afrotropical migratory system, knowledge of geographical wintering areas used by migrants that breed in Europe remains deficient, despite the advent of satellite transmitters and geolocators. Here we explored the use of theoretical plant δ13C and δ15N landscape distributions coupled with δ2H hydrologic models to construct multi-isotopic avian foodweb clusters for Africa. The cluster analysis identified four distinct regions of Africa based on all three isotopes (13C, 2H, 15N), and five regions based only on 13C and 15N. We applied known isotopic diet-tissue discrimination factors to map equivalent feather isotopic clusters for Africa. The validity of these feather isotopic clusters was tested by examining how well known- and unknown-origin species were placed in regions of Africa using previously published feather isotope data. The success of this multi-isotopic cluster model depended upon the species of interest and additionally on how well potential winter molt origins in Africa were constrained by prior information. Ground-truthing data suggested this approach will be useful for first-order approximation of overwintering regions for Afrotropical migrants and will be improved as our understanding of the nature of isoscapes for Africa is refined.