Microplastics (MPs) constitute a main environmental issue due to their threat to marine organisms and so far to humans. The lack of a fast standard protocol in MP isolation and identification from living organisms bring to challenge for the science. In this paper, an optimized protocol using potassium hydroxide 10% (KOH 10%; m/v) for digestion of mussel soft tissues (Mytilus edulis) and multi-steps of sedimentation has been developed. Efficiency higher than 99.9% of organic and mineral matter elimination was shown by application on mussels sampled on the French Atlantic coast. The identification of MPs was performed by FTIR microscopy straight on the filter and the whole analysis can be compatible with a routine goal. Fourteen MPs of four different chemical natures were found and identified in 5 pools of 3 sampled mussels. Their size ranged from 30 to 200 μm. Further investigations are now needed to evaluate the potential risk of such particles within this marine bivalve species and other filter feeders.