The aims of this study were to investigate the effect of temperature, time and stirring on changes in protein degree of hydrolysis (DH), free amino acids (FAA), lipid oxidation and total volatile basic nitrogen (TVB-N) during ensilaging of herring (Clupea harengus) filleting co-products. Results showed that temperature and time, and in some cases the interaction effect between these two factors, significantly influenced all the studied responses. Increasing ensilaging temperature and time from 17 to 37 °C and 3 to 7 days, respectively, increased DH, FAA, and TVB-N content from 44.41 to 77.28%, 25.31 to 51.04 mg/g, and 4.73 to 26.25 mg/100 g, respectively. The lipid oxidation marker 2-thiobarbituric acid reactive substances (TBARS) did not increase with time at temperatures above 22 °C, while 2-pentylfuran increased up to 37 °C. Based on the process parameters and responses investigated in this study, and considering energy requirements, it was suggested to perform ensilaging at ambient temperatures (i.e. around 20 °C) with continuous stirring at 10 rpm for 1-3 days; the exact length being determined by the desired DH.