The dioxin, dioxin-like polychlorinated biphenyl (DL-PCB), fat, and dry matter partitioning during fishmeal production have been studied in pilot scale. Most of the dry matter and lipid content in the fishmeal could be ascribed to the press cake intermediate product. Dioxins and DL-PCBs are fat-soluble compounds, and the process partitioning is reflected by the fat partitioning data. Enzyme and heat treatment of the press cake and stickwater concentrate did not improve fat separation. Soybean oil extraction of the press cake reduced the dioxin and DL-PCB content by 97%. Less exchange of fatty acids was observed (56-72%). Combined with fat separation of the stickwater concentrate, the applied process conditions were able to give a fishmeal decontamination rate higher than hexane and isopropanol extraction of the fishmeal. Quantification of fat content based on chloroform/methanol extraction was found to be the best protocol to estimate fat partitioning and decontamination effects. The oil extraction process requires further optimization, but has several advantages compared to organic solvent extraction. These include easy implementation in an existing fishmeal processing line, use of a safe and nonflammable extraction medium, and expected lower investment and operation costs. A new integrated fishmeal and fish oil production and decontamination process line is proposed.