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Microplastic (MP) has become ubiquitous in the marine environment. Its threat to marine organisms has been demonstrated under laboratory conditions, yet studies on wild populations still face methodological difficulties. We reviewed the methods used to separate MP from soft animal tissues and highlighted a lack of standardised methodologies, particularly critical for synthetic microfibres. We further compared enzymatic and a potassium hydroxide (KOH)-based alkaline digestion protocols on wild crabs (Carcinus aestuarii) collected from three coastal lagoons in the north Adriatic Sea and on laboratory-prepared synthetic polyester (PES) of different colour and polypropylene (PP). We compared the cost-effectiveness of the two methods, together with the potential for adverse quantitative or qualitative effects on MP that could alter the capability of the polymers to be recognised via microscopic or spectroscopic techniques. Only 5.5% of the 180 examined crabs contained MP in their gastrointestinal tracts, with a notably high quantitative variability between individuals (from 1 to 117 particles per individual). All MP found was exclusively microfibres, mainly PES, with a mean length (±SE) of 0.5 ± 0.03 mm. The two digestion methods provided comparable estimates on wild crabs and did not cause any visible physical or chemical alterations on laboratory-prepared microfibres treated for up to 4 days. KOH solution was faster and cheaper compared to the enzymatic extraction, involving fewer procedural steps and therefore reducing the risk of airborne contamination. With digestion times longer than 4 days, KOH caused morphological alterations of some of the PES microfibres, which did not occur with the enzymatic digestion. This suggests that KOH is effective for the digestion of small marine invertebrates or biological samples for which shorter digestion time is required, while enzymatic extraction should be considered as alternative for larger organisms or sample sizes requiring longer digestion times.