Producing fish silage for animal feed is an excellent way of valorizing underutilized fishery byproducts. However, the nutritional quality of fish silage strongly depends on the freshness and composition of the raw materials. The purpose of this study was to determine the effect of raw material composition (RMC) on nutritional quality and stability of fish silage. Using different combinations of whole undersized flatfish (plaice, sole, flounder) and codfish (whiting), four fish silages were produced: a single-species (plaice) flatfish silage (F-single); a mixed flatfish silage in equal ratios (F-equal); a mixed flatfish silage in ratios similar to fish-bycatch ratios (F-bycatch); a mixed flatfish and codfish silage, also in ratios similar to fish-bycatch ratios (FC-bycatch). Raw materials were homogenized, mixed with 2.5% (v/w) formic acid and 0.2% (w/w) potassium sorbate, and stored for 91 days at ambient temperature. Dry matter (DM) increased slightly during storage in all silages, from 228 ± 3.7 g/kg silage to 256 ± 3.6 g/kg silage; whereas ash content slightly decreased, from 192 ± 15.8 g/kg DM to 176 ± 13.1 g/kg DM. Crude protein did not differ in the raw materials (739 ± 18.9 g/kg DM), but decreased at different speeds in the silages. After 91 days, protein content of F-single and F-bycatch decreased to 621 ± 9.5 g/kg DM and 634 ± 18.8 g/kg DM, respectively, whereas F-equal and FC-bycatch decreased to 592 ± 6.7 g/kg DM and 580 ± 7.6 g/kg DM, respectively. Differences in protein decrease could be caused by the higher degree of hydrolysis in F-equal (60.6 ± 3.4%) and FC-bycatch (62.2 ± 2.3%), compared to F-single (51.6 ± 4.7%) and F-bycatch (52.9 ± 1.7%), after 91 days. Extended hydrolysis leads to overall deamination, also reflected by the decrease in essential amino acids (EAA) and increase in total volatile basic nitrogen. Crude lipid decreased in F-single and F-bycatch, but remained stable in F-equal and FC-bycatch. After 91 days, there were no more differences between the silages (58.0 ± 4.2 g/kg DM). The decrease in F-single and F-bycatch could be the result of lipid oxidation, also reflected by the TBARS value and decreased polyunsaturated fatty acid (PUFA). Overall there is a significant effect of RMC on nutritional quality and stability of fish silage. A more diverse mixture of raw materials improved nutritional quality, mainly in the form of EAA and PUFA, but was also more prone to deterioration by chemical and biological processes.