Amidoximated polyacrylonitrile nanofiber membranes (P-Oxime) were functionalized with a reactive green 19 (RG19, as a model dye waste), to remove lysozyme as a soluble microbial protein model. The P-Oxime-RG19 nanofiber membranes were applied to remove lysozyme in batch and flow modes. The most effective removal capacity of P-Oxime-RG19 nanofiber membranes for lysozyme in batch mode was 1126.37 mg/g. The performance of P-Oxime-RG19 nanofiber membranes for removal of lysozyme in flow mode was further investigated under different pH values, loading flow rates, and loading concentrations of lysozyme. The influences of process parameters on the shape of the breakthrough curve were analyzed, and the experimental results were fitted with various dynamic models to understand the removal behavior of P-Oxime-RG19 nanofiber membranes. The results illuminated the substantial variations in the dynamic binding characteristics of P-Oxime-RG19 nanofiber membranes, including breakthrough time, dynamic binding capacity, mass transfer zone length, and membrane bed utilization. The adsorbed lysozyme could be completely washed out from the dyed membrane using 1.5 M NaCl.