Microplastics (MPs) are carriers of persistent organic pollutants (POPs). The influence of MPs on the toxicokinetics of POPs was investigated in a feeding experiment on Atlantic salmon (Salmo salar), in which fish were fed similar contaminant concentrations in feed with contaminants sorbed to MPs (Cont. MPs); feed with virgin MPs and contaminated feed (1:1), and feed with contaminants without MPs (Cont.). The results showed that the salmon fillets accumulated more POPs when fed with a diet where contaminants were sorbed to the MPs, despite the 125–250 μm size MPs themselves passing the intestines without absorption. Furthermore, depuration was significantly slower for several contaminants in fish fed the diet with POPs sorbed to the MPs. Modelled elimination coefficients and assimilation efficiencies of lipophilic chlorinated and brominated contaminants correlated with contaminant hydrophobicity (log Kow) within the diets and halogen classes. The more lipophilic the contaminant was, the higher was the transfer from feed to salmon fillet. The assimilation efficiency for the diet without MPs was 50–71% compared to 54–89% for the contaminated MPs diet. In addition, MPs caused a greater proportional uptake of higher molecular weight brominated congeners. In the present study, higher assimilation efficiencies and a significantly higher slope of assimilation efficiencies vs log Kow were found for the Cont. MPs diet (p = 0.029), indicating a proportionally higher uptake of higher-brominated congeners compared to the Cont. diet. Multiple variance analyses of elimination coefficients and assimilation efficiencies showed highly significant differences between the three diets for the chlorinated (p = 2E-06; 6E-04) and brominated (p = 5E-04; 4E-03) congeners and within their congeners. The perfluorinated POPs showed low assimilation efficiencies of 12%, which can be explained by faster eliminations corresponding to half-lives of 11–39 days, as well as a lower proportional distribution to the fillet, compared to e.g. the liver.