In this study, ensilaging of herring (Clupea harengus) filleting co-products was taken from lab-scale to pilot scale (1500 L) while monitoring the protein degree of hydrolysis (DH) and lipid oxidation. Subsequently, the possibility of recovering fish oil and protein hydrolysates using batch centrifugation at different g-forces/times was investigated. Around 38% DH was recorded after 2-day pilot-scale ensilaging of herring co-products at ambient temperature (i.e., ~ 22 °C), which was similar to the DH found in lab-scale (40% after 2 days; 22 °C). The lipid oxidation marker 2-thiobarbituric acid reactive substances (TBARS) reached 20 µmole TBARS/kg silage after 2-day ensilaging. Centrifugation of the silage at 3000–8500 × g for 2–20 min revealed successful separation into fish oil and protein hydrolysates. Heat-treating the silage (85 °C; 30 min) prior to centrifugation resulted in significantly higher oil and hydrolysates recoveries; the same being true for increased g-force. At 8500 × g, the recovery of oil and hydrolysates were 9.7 and 53.0% w/w, respectively, from heat-treated silage, while recoveries were 4.1 and 48.1% w/w, respectively, from non-heat treated silage. At 4500 × g, being a more scalable approach, corresponding numbers were 8.2 and 47.1% (w/w) as well as 2.0 and 40.2% (w/w). The recovered fish oil contained 8% EPA and 11% DHA of total fatty acids. Free fatty acids (FFA), peroxide value (PV), p-anisidine value (p-AV), and total oxidation (TOTOX) values of oils were in the range of 4–7% (FFA), 3.6–3.7 meq/kg oil (PV), 2.5–4.0 (p-AV), and 9.9–11.1 (TOTOX), respectively, which were within the acceptable limits for human consumption specified by the GOED voluntary monograph. The recovered protein hydrolysates contained peptides in the molecular weight range 0.3–6 kDa (~ 37%) and 11–34 kDa (~ 63%). Also, the remaining solids contained 15–17% (w/w) protein, having 44–45% essential amino acids. Overall, the results suggest that herring co-product silage is a valuable source of fish oil and protein hydrolysates, paving the way for ensilaging based-biorefining of herring co-products into multiple products.