Robust and reproducible quantification of microplastic pollution in freshwater ecosystems requires the processing of a large amount of samples collected in varying environmental conditions. Such samples are characterized by a high amount of organic matter compared to microplastics and are highly variable in terms of the quantity and the composition of matrices, requiring a standardized analytical protocol for sample treatment and analysis. However, two important and time-consuming steps for microplastic recovery are the elimination of organic matter and microscopic inspection of samples. Here, we developed and validated a protocol, targeting particles with length ranging from 700 µm to 5 mm, that includes a double-step digestion of organic matter, consisting of incubation with potassium hydroxide followed by hydrogen peroxide solutions, and two stereomicroscopic analyses. In addition, we developed several technical improvements allowing reducing the time needed to process samples, such as the design of an adapted filter-cap to improve the content transfer. The absence of physical and chemical alterations in the investigated microplastic pellets and the average reduction of 65.8% (± 9.59 SD) of organic matter in real samples demonstrated that our protocol is fit for purpose. We recommend a second stereomicroscopic analysis to avoid underestimating microplastic concentration and particle size distribution biased towards larger particles. When used for a large-scale monitoring of microplastic pollution, this protocol resulted in an estimated time of 38 h for one person for the treatment of a batch of 24 samples, allowing a higher throughput sample processing and reproducible quantification. • Protocol customization towards high-throughput sample processing • Double step digestion to improve organic matter elimination • Importance of stereomicroscopic analysis for microplastic recovery