Standardisation and validation of methods for microplastics research is essential. A major methodological challenge is the removal of planktonic organisms from marine water samples allowing for the identification of microplastics associated to planktonic communities. To improve the reproducibility and accuracy of digestion methods for the removal of planktonic biomass, we compared and modified existing chemical digestion methods. These digestion methods included an acidic digestion using nitric acid, alkaline digestions with potassium hydroxide (alkaline 1 digestion) and sodium hydroxide from drain cleaner (alkaline 2 digestion), an oxidative digestion using sodium dodecyl sulfate with hydrogen peroxide, and an enzymatic digestion using enzyme drain clean pellets. Chemical digestion of three densities of zooplankton communities (high, medium, and low) in the presence of five commonly found environmental microplastic pollutants (polyamide, polyethylene, polyethylene terephthalate, polypropylene, and polystyrene) were performed for each treatment. The chemical treatments were assessed for (i) their digestion efficiency of zooplankton communities by different biomass densities, and (ii) their impact on microplastic particles through the comparison of both chemical (Raman spectroscopy) and physical (length, width, and visual) changes, between the pre-treatment and post-treatment microplastic particles. The alkaline 1, alkaline 2 and oxidative methods demonstrated significantly better digestion efficiency (p < 0.05) than the modified enzymatic and acidic treatments. The acidic, alkaline 1, and alkaline 2, treatments caused the most damages to the microplastic particles. We suggest future studies to implement the oxidative digestion method with sodium dodecyl sulfate and hydrogen peroxide because of its high digestion efficiency, and low damage to microplastic particles. This method is similar to the wet peroxide oxidation digestion method used throughout the literature but can be implemented at a lower cost.