Currently, the evidence of the ingestion of microplastics (MPs) by organisms or the accumulation in different environmental compartments has been achieved using several methodological procedures. However, its uses have not been standardized across studies. In this study, we aim to assess and validate a protocol that can be useful for optimizing the identification and quantification procedures of polyethylene microplastics (PE MPs) in biological samples. Initially, considering that numerous studies filter samples previously digested in cellulosic membranes for isolation and analysis of MPs, we evaluated whether washing these membranes with different reagents could contribute to the complete detachment of particles, as well as to their dispersion in the obtained solutions. However, none of the tested reagents (dimethyl sulfoxide, acetone, ethyl alcohol and chloroform), including purified water, was able to completely remove the MPs adhered to the membranes or facilitate their dispersion in the solutions. On the other hand, we observed that the digestion of the membranes by acetonitrile constituted a procedure that prevents the loss of particles due to adherence, in addition to promoting good dispersion of MPs. Subsequently, we evaluated the use of Neubauer chambers for the quantification of MPs, having observed a good recovery rate (>92%) and results with insignificant variation, in PE MPs solutions with different concentrations (0.15; 0.075 and 0.0375 mg/mL). Ultimately, the validation of the proposed procedures took place from the evaluation of the accumulation of PE MPs in Astyanax spp. juveniles, having demonstrated the efficiency and sensitivity of the method proposed for this purpose. Subsequently, our study provides a methodological alternative that can optimize MPs quantifications in biological samples and reduce the generation of biased or unreliable results.