Microplastic quantification in marine vegetated ecosystems remains analytically demanding, yet little is known about the environmental footprint of the laboratory procedures required to isolate and measure these particles. This study applies Life Cycle Assessment (LCA) to laboratory analytical workflows for microplastics quantification, focusing exclusively on sample preparation and analytical procedures rather than natural environmental absorption or fate processes, in two ecologically relevant matrices: (i) pelagic algae (Sargassum) and (ii) seagrass biomass. Using openLCA 2.5 and the ReCiPe Midpoint (H) v1.13 method, the analysis integrates foreground inventories of digestion, filtration, drying, and spectroscopic identification, combined with background datasets from OzLCI2019, ELCD 3.2 and USDA. Results show substantially higher impacts for the algae scenario, particularly in climate change, human toxicity, ionising radiation and particulate matter formation, largely driven by longer digestion times, increased reagent use and higher energy demand during sample pre-treatment. Conversely, the seagrass scenario exhibited lower burdens per functional unit due to reduced organic complexity and shorter laboratory processing requirements. These findings highlight the importance of matrix-specific methodological choices and the influence of background datasets on impact profiles. The study provides a first benchmark for the environmental performance of microplastic analytical workflows and underscores the need for harmonised, low-impact laboratory protocols to support sustainable monitoring of microplastic pollution in marine ecosystems.