Failing to package and preserve food safely causes contamination and the waste of many food materials. To address this point, in this study, an electrospun water-based polyurethane material with a biocompatible and air-permeable texture was prepared to be used as a food packaging material. For this purpose, a waterborne polyurethane (WBPU) was synthesized through melt polymerization using biocompatible polymers, such as poly-(caprolactone diol) and poly(ethylene glycol) as soft segments and lysine diisocyanate as a hard segment, followed by emulsifying with L-lysine aqueous solution in the absence of a catalyst. Then, the electrospinning of the WBPU was conducted to obtain a fibrous film-like material without contributing any additive polymer to the solution. The conditions yielding the most suitable electrospun nanofibrous network tissue were investigated by changing the molecular mass and mole ratio of soft segment polymers used in the synthesis and the type of diol molecules, such as 1,3-propanediol, 1,4-butanediol, and glycerol, used as a chain extender in detail. Structural, thermal, morphological, and mechanical properties of WBPU nanofibers were determined by attenuated total reflectance−Fourier transform infrared, 1 H NMR, GPC, DSC, scanning electron microscopy, contact angle measurement, and tensile test, respectively. The samples' biodegradability and cytotoxicity were demonstrated by burying them in garden soil for a week and the MTT test, respectively. Finally, the usability of the WBPU nanofibrous mesh tissue as food packaging was investigated by covering bananas. The main contribution of this work is the development of a soil-degradable, biocompatible, and air-permeable WBPU nanofibrous material suitable for food packaging applications that can potentially reduce food contamination and waste.