As concern over plastic pollution grows, numerous organisations are actively monitoring microplastics in marine and coastal environments. However, inconsistent methods for sampling, analysis, and reporting are impacting effective research and the integration of data. Here we present our harmonised manual for investigating microplastics across four key environmental matrices: sediment, water, biota, and air, with particular focus on the sampling of fish. Published as part of the National Environmental Science Programme’s ‘Field manuals for marine sampling to monitor Australian waters’ we provide essential criteria and workflows for sampling design and collection, along with best practice recommendations for processing, quantifying, and characterising microplastics. We will share guidelines for quality assurance, quality control, and standardised reporting to ensure data consistency and comparability. By following these standardised methods and adopting Findable, Accessible, Interoperable, and Reusable (FAIR) workflows, researchers, industry professionals, regulatory bodies, and non-government organisations can generate harmonised data crucial for informed decision-making. This approach will enhance our ability to synthesise global datasets and advance our understanding of microplastic impacts on fish and other marine organisms.