The present study impacts the growing knowledge about co-products obtained from the primary processing of Atlantic salmon (Salmo Salar L.) as food ingredients by highlighting their microbial and chemical composition and stability. The proximate composition varied between the co-products from the fatty belly-flap (34% lipid, 15% protein) to the leaner deboned meat (10% fat, 22% protein) (p < 0.001), whereas no differences were observed between the superior and production qualities (p > 0.31). However, the co-products from the processing of production quality salmon had a higher microbial load of psychotropic aerobic-, H2S-producing- and Pseudomonas spp. bacteria than those of superior quality salmon origin (4.0, 5.2, and 4.3 log CFU/g units higher, respectively). Fatty co-products, such as the belly flap, were especially susceptible to ATP degradation, giving higher Hx concentrations after 7/10 days of ice-storage than leaner fractions (p < 0.001). Moreover, a positive correlation between the lipid level and degradation of ATP was observed (r = 0.62, p = 0.006). To conclude, co-products from superior and production quality salmon contain valuable nutrients suitable for human consumption. However, the co-products are vulnerable to microbial and chemical deterioration, presumably due to disruption of biological membranes during processing, and should be handled accordingly.