The occurrence of persistent organic pollutants (POPs) in the Arctic has been of constant concern, as these chemicals cause reproductive effects and mortality in organisms. The Arctic acts as a chemical sink, which makes this system an interesting case for bioaccumulation studies. However, as conducting empirical studies for all Arctic species and POPs individually is unfeasible, in silico methods have been developed. Existing bioaccumulation models are predominately validated for temperate food chains, and do not account for a large variation in trophic levels. This study applies Monte Carlo simulations to account for variability in trophic ecology on Svalbard when predicting bioaccumulation of POPs using the optimal modeling for ecotoxicological applications (OMEGA) bioaccumulation model. Trophic magnification factors (TMFs) were calculated accordingly. Comparing our model results with monitored POP residues in biota revealed that, on average, all predictions fell within a factor 6 of the monitored POP residues in biota. Trophic variability did not affect model performance tremendously, with up to a 25% variability in performance metrics. To our knowledge, we were the first to include trophic variability in predicting biomagnification in Arctic ecosystems using a mechanistic biomagnification model. However, considerable amounts of data are required to quantify the implications of trophic variability on biomagnification of POPs in Arctic food webs.