The knowledge of composition and strain with high spatial resolution is highly important for the understanding of the chemical and electronic properties of alloyed nanostructures. Several applications require a precise knowledge of both composition and strain, which can only be extracted by self-consistent methodologies. Here, we demonstrate the use of a quantitative high resolution transmission electron microscopy (QHRTEM) technique to obtain two-dimensional (2D) projected chemical maps of epitaxially grown Ge-Si:Si(001) islands, with high spatial resolution, at different crystallographic orientations. By a combination of these data with an iterative simulation, it was possible infer the three-dimensional (3D) chemical arrangement on the strained Ge-Si:Si(001) islands, showing a four-fold chemical distribution which follows the nanocrystal shape/symmetry. This methodology can be applied for a large variety of strained crystalline systems, such as nanowires, epitaxial islands, quantum dots and wells, and partially relaxed heterostructures.