Nanowire growth enables creation of embedded heterostructures, where one material is completely surrounded by another. Through materials-selective post-growth oxidation it is also possible to combine amorphous oxides and crystalline, e.g., III-V materials. Such oxide-embedded structures pose a challenge for compositional characterization through transmission electron microscopy since the materials will overlap in projection. Furthermore, materials electrically isolated by an embedding oxide are more sensitive to electron beam-induced alterations. Methods that can directly isolate the embedded material, preferably at reduced electron doses, will be required in this situation. Here, we analyse the performance of two such techniques – local lattice parameter measurements from high resolution micrographs and bulk plasmon energy measurements from electron energy loss spectra – by applying them to analyse InP-AlInP segments embedded in amorphous aluminium oxide. We demonstrate the complementarity of the two methods, which show an overall excellent agreement. However, in regions with residual strain, which we analyse through molecular dynamics simulations, the two techniques diverge from the true value in opposite directions.