Heterogeneous integration of semiconductors combines the functionality of different materials, enabling technologies such as III−V lasers and solar cells on silicon and GaN LEDs on sapphire. However, threading dislocations generated during the epitaxy of these dissimilar materials remain a key obstacle to the success of this approach due to reduced device efficiencies and reliability. Strategies to alleviate this and understand charge carrier recombination at threading dislocations now need an accurate description of the structure of threading dislocations in semiconductor heterostructures. We show that the composition around threading dislocations in technologically important InGaAs/GaAs/Ge/ Si heterostructures are indeed different from that of the matrix. Site-specific atom probe tomography enabled by electron channeling contrast imaging reveals this at individual dislocations. We present evidence for the simultaneous fast diffusion of germanium and indium up and down a dislocation, respectively, leading to unique compositional profiles. We also detect the formation of clusters of metastable composition at the interface between Ge and GaAs, driven by intermixing in these two nearly immiscible materials. Together, our results have important implications for the properties of dislocations and interfaces in semiconductors and provide new tools for their study.