The species composition of fish burgers - declared as composed by European seabass (Dicentrarchus labrax) - collected in the context of a seafood company self-control was assessed using metabarcoding. Positive/negative controls, replicates, samples processed in dirty laboratory environment were also included as quality measures. A ≈ 200 bp of the 16S rRNA gene was selected as molecular target. The sequencing was performed on Illumina platform, and the data were analysed using DADA2 R package. The species taxonomic assignment was performed using Blastn against GenBank (identity value ≥ 99 %). The sequences assigned to D. labrax were highly predominant in all the products, with percentages ≥ 99.34 %, except for one, where also a high number of sequences assigned to Atlantic salmon (Salmo salar) were found (12.41 %). Sequences identified with other species (seafood, mammals, insects) were in percentage ≤ 0.57 %, and in the 14 % of the cases they even did not achieve the 0.001 %. A threshold value of 3.3 % to remove false positives was fixed based on the results of the positive controls. Overall, metabarcoding was proved as effective technique to assess the ingredients contained in complex seafood products. However, further investigation including a higher sample number and inter-laboratory validation should be performed to validate the procedure. •The species composition of fish burgers was assessed using metabarcoding.•A number of experimental controls was included to assess the process quality.•A threshold value to adjust the data respect to DNA contamination was established.•All the products except for one were compliant respect to the declared ingredient.•Standard Operating Procedures should be defined to harmonize protocols.