The biofiltration capacity of bivalve populations is known to alleviate the effects of coastal eutrophication. However, this important ecosystem service could potentially be impaired by the increasing microplastic abundance in near shore environments. It is known that relatively large microplastics (∼500 μm) impair the filtration capacity of bivalves. However, the effect of smaller microplastics, and specifically microfibers, is not known even though they are more common in many natural systems and similar in size to phytoplankton, the main food source of mussels. Here, we investigated the effects of long-term exposure to microfibers (MFs), which are smaller than 100 μm, on the biofiltration capacity of the blue mussel, Mytilus edulis. Our findings show that long-term exposure (here 39 days) to microfibers significantly reduced (21%) the clearance of phytoplankton (Tetraselmis sp). While previous studies have shown that larger microplastics can decrease the filtration capacity of mussels after short-term exposure, our findings suggest that, for smaller MFs, mussel’s clearance capacity is significantly affected after long-term exposure (39 days in this study). This may be due to the accumulation of MFs in the digestive system. In addition, the most efficient phytoplankton consumers were more susceptible to MF accumulation in the digestive system. This suggests that prolonged exposure to MF of coastal mussels could negatively impact the biofiltration of more potent individuals, thus decreasing the ecosystem service potential of the population as a whole.