Single‐cell nanoencapsulation (SCNE), a chemical strategy for sustaining the structure and functions of viable cells, strictly requires, for creation of cell‐in‐shell structures, materials that are extremely compatible with chemically labile cells. In this study, we propose the utilization of eggshell membrane hydrolysates (ESMHs) and coffee melanoidins (CMs) derived from food waste—eggshells and spent coffee grounds, respectively—as layer‐by‐layer (LbL) components. Hydrogen bonding‐based LbL construction of nanoshells on Saccharomyces cerevisiae proves greatly biocompatible, not harming the cells (viability > 99%). The ESMH/CM films are durable in a wide range of pH values and effectively protect the encapsulated cells from lethal heavy metals (Cd2+, Cu2+, and Zn2+) and UV‐B irradiation. The Fe3+‐mediated shell cross‐linking augments the ESMH/CM shell's durability and cytoprotectability. The natural ESMHs and CMs will add to the biomaterial arsenal for a multitude of applications that involve the interfacing of living cells and materials.