The study aimed to provide insight into the lipid quality of pelagic fishmeal and fish oil processing of mackerel and herring cut-offs, and the effect of temperature changes in the cooker (85−95 °C) during production. Samples were collected after each processing step at a traditional processing line where water and lipid content, free fatty acids (FFA), phospholipids (PL) and fatty acid composition (FAC) were measured. Results showed that the standard procedures at 90 °C included ineffective draining and concentration steps. Moreover, the solid streams entering the driers variated in chemical composition, suggesting that processing each stream separately could be beneficial for maintaining the lipid quality. The cooking temperature affected the lipid removal from the fishmeal processing, where lowering the temperature to 85 °C resulted in a lower lipid content of the final fishmeal, along with lower FFA and PL values. Hence, the fishmeal and fish oil factories could save energy by lowering the cooking temperature, as well as obtaining more stable and higher value products. Further recommendations include more focus on the initial steps for a better homogenization and breakdown of the raw material, as well as investigation of different drying techniques applied on each processing stream entering the drying steps.