Small plastic particles are found ubiquitously in marine and freshwater ecosystems and consequently, their inhabitants. When aquatic animals are consumed as seafood, human exposure to those plastic particles is possible. However, only a few studies, applying largely different analytical procedures, assessed microplastics content in the edible part of seafood. In this study, ten protocols for the extraction of microplastics from biota were chosen and tested for their suitability to digest the edible part of a broad range of seafood species. The following criteria were used for this assessment: 1) feasibility to filtrate the entire digested sample with one filter of approximately 1 μm pore size, 2) effect of reagents applied during the sample preparation on the polymer integrity as assessed by means of infrared and Raman spectroscopy as well as pyrolysis gas chromatography mass spectrometry, 3) total sample preparation time and the possibility to avoid the use of expensive reagents. The most suitable protocol was found to be an enzymatic-alkaline approach, consisting of a quick hydrolysis of proteins with pepsin for 2 h and a consecutive alkaline hydrolysis for 4 h, both at 37 °C for most of the tested seafood species. Digestion efficiency of the optimised protocol was tested with fish fillets and soft tissues of commercially relevant molluscs and crustacean species. Compared to most other protocols described in literature, an adequate digestion of the seafood matrix was achieved faster without being significantly more cost- or labour-intensive. Moreover, only negligible degradation of eleven commercially relevant polymers excluding polyacrylonitrile was observed. Polymer integrity was assessed by a change in particle weight or surface as well as spectroscopic and chromatographic data. The optimised sample preparation protocol aims to support future method standardisation efforts in order to assess the dietary uptake of microplastics in humans.