Abstract: The interplay between strain and composition is at the basis of heterostructure design to engineer new properties. The influence of the strain distribution on the incorporation of indium during the formation of multiple InGaN/GaN quantum dots (QDs) in nanowire (NW) heterostructures has been investigated, using the combined techniques of geometric phase analysis of atomic-resolution images and quantitative elemental mapping from core-loss electron energy-loss spectroscopy within scanning transmission electron microscopy. The variation in In-content between successive QDs within individual NWs shows a dependence on the magnitude of compressive strain along the growth direction within the underlying GaN barrier layer, which affects the incorporation of In-atoms to minimize the local effective strain energy. Observations suggest that the interfacial misfit between InGaN/GaN within the embedded QDs is mitigated by strain partitioning into both materials, and results in normal stresses inflicted by the presence of the surrounding GaN shell. These experimental measurements are linked to the local piezoelectric polarization fields for individual QDs, and are discussed in terms of the photoluminescence from an ensemble of NWs.