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Colloidal drug delivery systems often face physical and chemical instability as well as challenges with directed delivery. In order to overcome these challenges the colloidal formulations can be processed into microparticulate form (nanoembedded microparticles (NEMs)). In this study, different polymer nanocarriers (poly(lactide-co-glycolide), poly(styrene), chitosan and dendrimers) were used for preparing NEMs by spray-drying. Further, distinct matrix excipients were investigated including sugars (i.e., trehalose, sucrose, mannitol) and polymers (poly(vinyl pyrrolidone) and poly(ethylene glycol)), and the characteristics and performance of NEMs were studied in detail. It was found that with increasing hydrophilicity of the polymer nanocarriers, an increasing amount of excipient was necessary to stabilize the nanoparticles. NEMs containing polyplexes and nanogels required a matrix-to-nanoparticle (M:N) ratio of 50:1 and 10:1, respectively, whereas NEMs with poly(styrene) and poly(lactide-co-glycolide) only required an M:N ratio of 1:1 and 1:4, respectively. Investigation of different excipients demonstrated that water soluble sugars and polymers can be used to prepare NEMs and that spray-dried amorphous excipients (trehalose, sucrose, poly(vinyl pyrrolidone)) are superior to spray-dried crystalline excipients (mannitol, poly(ethylene glycol)) for stabilizing NEMs. It is therefore important to select an appropriate excipient for stabilization of a given nanoparticle system and identify a suitable level of this excipient to keep the nanoparticles viable.