In this paper, a natural polymer, zein, is converted into a disposable and environmentally friendly surface enhanced Raman spectroscopy (SERS) biosensor platform to detect toxins. First, protein nanofiber mats were fabricated using electrospinning. Next, the surface of the fibers was decorated with metallic nanoparticles to create hotspots for the detection of the target molecule. Four types of metallic nanoparticles were tested for sensitivity optimization: gold, silver, silver‐shelled‐gold, and a mixture of gold and silver nanoparticles. Silver‐shelled‐gold nanoparticles gave the highest SERS intensity, and at the concentration of 1012 particles/ml, the highest enhancement factor (EF) of 2.49 × 106 was reached, which is the highest EF ever reported for a zein‐based biodegradable platform. Acrylamide was used as the model food carcinogenic toxin and its detection with this nanofiber‐based platform gave a limit of detection of 2.06 ng/ml. This LOD is 104 times lower than the limit of detection that was achieved previously with a zein‐based SERS platform. Other sensitive analytical methods (GC–MS and LC–MS/MS) gave LODs of 5–10 and 20–50 ng/ml for acrylamide, much higher than the method used in this study. This sensitivity is much lower than any other previous attempts to detect acrylamide with biodegradable sensors.