Abstract Norway's fish processing industry generates large amounts of fish waste every year. The high-risk waste fraction with most of its oil removed has not yet been tested for energy production. The stability of an anaerobic digestion process that incorporates this material with steam exploded Salix and cow manure was tested using mesophilic, semi-continuous laboratory-scale digesters. The effects of recycling the liquid digestate fraction were also investigated. The removal of ammonium (NH4+) and phosphate (PO43−) from the rejected digestate using struvite precipitation and bentonite adsorption were tested to generate a nutrient-enriched, final solid fertiliser. Adding 20% fish by-product (volatile solids basis) increased methane yields by 35%, while recycling the digestate caused a slight increase. The NH4+–N levels reached 4–5 g l−1 in the reactors with recirculation and fish feed. Although these levels may threaten methanogenesis, the stability of the process was maintained during the entire period due to the good balance between the lignocellulose, proteins and fats provided by the co-digestion mixture and the positive effects of recirculation. The NH4+ and PO43− were successfully removed from the rejected liquid digestate. The reductions using struvite reached 87% and 60% (pH 9.5 and Mg2+:NH4+:PO43− ratio of 1.2:1:1), while bentonite achieved 82% and 52%, respectively.