Protein wasted by the disposal of fish processing by-products may be recovered using isoelectric solubilization and precipitation. Extreme pH shifts are used to solubilize the protein and then it is recovered by precipitation and centrifugation. Microbial survival after this process is unknown; therefore, the purpose was to see if Listeria innocua would survive extreme pH shifts during the protein recovery process. Fresh rainbow trout fillets were inoculated with L. innocua, homogenized, and brought to the target pH of 2, 3, 11.5, or 12.5 by the addition of concentrated hydrochloric acid or sodium hydroxide. The proteins were allowed to solubilize at 4 degrees C for 10 min, centrifuged, and the lipid and insoluble components (bones, skin, insoluble protein, and so on) were removed. A 2nd pH shift (pH 5.5) and centrifugation was used to separate the precipitating protein and water fractions. Each constituent (lipid, protein, water, insoluble components) was analyzed for bacterial content using growth and selective media. The sums of the surviving L. innocua in these constituents were compared to the initial inoculum. There were no significant differences in recovery on growth or selective media (P > 0.05). The greatest loss occurred when the pH was shifted to 2, with a 3.1-log reduction in the combined fractions of the trout fillets and a 3.8-log reduction in the protein fraction. There were no significant losses when the pH was adjusted to 11.5 (P > 0.05). Future studies will continue to look at the effects of using organic acid, rather than inorganic, for protein solubilization.