Phosphopeptide enrichment based on metal oxide affinity chromatography is one of the most powerful tools for studying protein phosphorylation on a large scale. To complement existing metal oxide sorbents, we have recently introduced tin dioxide as a promising alternative. The preparation of SnO(2) microspheres by the nanocasting technique, using silica of different morphology as a template, offers a strategy to prepare materials that vary in their particle size and their porosity. Here, we demonstrate how such stannia materials can be successfully generated and their properties fine-tuned in order to obtain an optimized phosphopeptide enrichment material. We combined data from liquid chromatography-mass spectrometry experiments and physicochemical characterization, including nitrogen physisorption and energy-dispersive X-ray spectroscopy (EDX), to explain the influence of the various experimental parameters.