Microplastic debris (<5 mm) is a prolific environmental pollutant, found worldwide in marine, freshwater and terrestrial ecosystems. Interactions between biota and microplastics are prevalent, and there is growing evidence that microplastics can incite significant health effects in exposed organisms. To date, the methods used to quantify such interactions have varied greatly between studies. Here, we critically review methods for sampling, isolating and identifying microplastics ingested by environmentally and laboratory exposed fish and invertebrates. We aim to draw attention to the strengths and weaknesses of the suite of published microplastic extraction and enumeration techniques. Firstly, we highlight the risk of microplastic losses and accumulation during biotic sampling and storage, and suggest protocols for mitigating contamination in the field and laboratory. We evaluate a suite of methods for extracting microplastics ingested by biota, including dissection, depuration, digestion and density separation. Lastly, we consider the applicability of visual identification and chemical analyses in categorising microplastics. We discuss the urgent need for the standardisation of protocols to promote consistency in data collection and analysis. Harmonized methods will allow for more accurate assessment of the impacts and risks microplastics pose to biota and increase comparability between studies.