Biological composites offer self-healing properties, biocompatibility, high responsivity to external stimuli, and multifunctionality, due, in part, to their complex, hierarchical microstructure. Such materials can be inexpensively grown, and self-assembled from the bottom up, enabling democratized, sustainable manufacturing routes for micro- and nano-devices. While biological composites have been shown to incorporate rich photonic structures, their phononic properties have hitherto remained unexplored. In this study, we demonstrate that biological composites in the form of micron-thick decellularized onion cell scaffolds behave as an organic phononic material, with the presence of band gaps forbidding the propagation of elastic waves in select frequency ranges. We show that the onion cells’ phononic properties can be phenotypically tuned, and anticipate these findings will yield new biologically-derived, “green,” and genetically tailorable phononic materials.