Specific therapeutic targeting of kidney podocytes, the highly differentiated ramified glomerular cells involved in the onset and/or progression of proteinuric diseases, could become the optimal strategy for preventing chronic kidney disease. With this aim, we developed a library of engineered polymeric nanoparticles (NPs) of tuneable size and surface properties and evaluated their interaction with podocytes. NP cytotoxicity, uptake, and cytoskeletal effects on podocytes were first assessed. On the basis of these data, nanodelivery of dexamethasone loaded into selected biocompatible NPs was successful in repairing damaged podocytes. Finally, a three-dimensional in vitro system of co-culture of endothelial cells and podocytes was exploited as a new tool for mimicking the mechanisms of NP interaction with glomerular cells and the repair of the kidney filtration barrier.