The Mediterranean Sea is greatly affected by marine litter. In this area, research on the impact of plastic debris (including microplastics) on biota, particularly large filter-feeding species such as the fin whale (Balaenoptera physalus), is still in its infancy. We investigated the possible overlap between microplastic, mesoplastic and macrolitter accumulation areas and the fin whale feeding grounds in in a pelagic Specially Protected Area of Mediterranean Importance (SPAMI): the Pelagos Sanctuary. Models of ocean circulation and fin whale potential habitat were merged to compare marine litter accumulation with the presence of whales. Additionally, field data on microplastics, mesoplastics, and macrolitter abundance and cetacean presence were simultaneously collected. The resulting data were compared, as a multi-layer, with the simulated distribution of plastic concentration and the whale habitat model. These data showed a high occurrence of microplastics (mean: 0.082 items/m2, STD ± 0.079 items/m2) spatial distribution agreed with our modeling results. Areas with high microplastic density significantly overlapped with areas of high macroplastic density. The most abundant polymer detected in all the sampling sites was polyethylene (PE), suggesting fragmentation of larger packaging items as the primary source. To our knowledge, this is the first study in the Pelagos Sanctuary in which the simulated microplastic distribution has been confirmed by field observations. The overlap between the fin whale feeding habitat and the microplastic hot spots is an important contribution for risk assessment of fin whale exposure to microplastics.