Hypothesis: Spray drying is a facile technique to transform colloidal dispersion into micro-granules of controlled size, shape, and morphology. There is significant interest to understand the structural integrity, different morphology of the granules obtained post spray drying which find potential application in many technological fields. The shape of the constituent particles in the colloidal dispersion that is spray dried is expected to influence the micro-structural features of the micro-granules. Experiments: We investigate the formation of micro-granules consisting of nano-ellipsoids through controlled spray drying. The morphological features and the packing of ellipsoids in the granules are quantitatively analyzed by using small angle neutron scattering, small angle X-ray scattering and high-resolution field emission scanning electron microscopy. The time evolution of the micro-structure and the structural integrity of the granules are investigated by re-dispersing the powder granules in water. Findings: The morphology of the granules are found to be strongly correlated with the aspect ratio of the ellipsoid. While the drying of droplets containing lower aspect ratio ellipsoids give rise to mostly spherical granules, in stark contrast, for higher aspect ratio ellipsoids, micro-granules of different morphologies are formed including doughnut shaped granules. A plausible mechanism explaining such an aspect ratio dependent shape transformation is proposed. © 2019 Elsevier Inc.