Nanocoating of individual mammalian cells with polymer layers has been of increasing interest in biotechnology and biomedical engineering applications. Electrostatic layer-by-layer (LbL) deposition of polyelectrolytes on negatively charged cell surfaces has been utilized for cell nanocoatings using synthetic or natural polymers with a net charge at physiological conditions. Here, our previous synthesis of silk-based ionomers through modification of silk fibroin (SF) with polyglutamate (PG) and polylysine (PL) was exploited for the nanocoating of mammalian cells. SF-PL constructs were cytotoxic to mammalian cells, thus an alternative approach for the synthesis of silk ionomers through carboxylation and amination of regenerated SF chains was utilized. Through the optimization of material properties and composition of incubation buffers, silk ionomers could be electrostatically assembled on the surface of murine fibroblasts and human mesenchymal stem cells (hMSCs) to form nanoscale multilayers without significantly impairing cell viability. The resulting silk-based protein nanoshells were transient and degraded over time, allowing for cell proliferation. The strategies presented here provide a basis for the cytocompatible nanoencapsulation of mammalian cells within silk-based artificial cell walls, with potential benefits for future studies on surface engineering of mammalian cells, as well as for utility in cell therapies, 3D printing, and preservation.