The success of lithium-ion batteries (LIBs) and their unique advantages for electrochemical energy storage have sped up research in this field. A critical component of LIBs is the separator. Here, Bombyx mori silk cocoon separators have been treated with oxygen (O2) and nitrogen (N2) plasmas at different exposure times. The goal was to improve the electrochemical characteristics of these natural separators, without jeopardizing the major attributes of silk fibers. Major physical and chemical modifications have been identified at the submicrometer scale on the application of the plasmas: (1) Etching of the silk nanofibrils and concomitant increase of roughness (more effective with O2 plasma), corresponding to the destruction of the 5th structural hierarchy level of the silk fibers. (2) Creation of oxygen-containing functional groups carrying negative charges at the surface, causing a superhydrophobic-to-superhydrophilic transition, and favoring Li+ transport. The optimized cocoon separator exposed to O2 plasma for 30 s exhibited high electrolyte uptake (289%), high ionic conductivity (2.33 mS/cm at 25 °C), and low overall resistance. A cathodic half-cell of carbon-coated lithium iron phosphate incorporating this separator sample soaked in the ethylene carbonate/dimethyl carbonate/lithium hexafluorophosphate electrolyte demonstrated a performance boost with respect to the battery, including a raw cocoon separator: an outstanding increase (ca. 270%) of the discharge capacity (from 26.1 to 96.7 mAh/g at 5C-rate) and an impressive increase (291%) of the capacity retention (from 22.3% to 87.2%, from C/5 to 5C). This work proves that the O2 plasma exposure is a valid, simple, fast, clean, and safe top-down methodology to improve the properties of B. mori cocoon separators. The features of these plasma-treated separators, which surpass those of commercial separators, help in upgrading the performance of LIBs. This plasma-enhanced natural biomaterial separator technological platform pushes LIBs to the next performance-level, while guaranteeing the eco-friendly, sustainability, and safety labels.