Microplastics are widespread contaminants that still lack standardized methods for their assessment. While most research includes a visual method of identification, the challenge increases when sampling smaller microplastics. Staining dyes, such as Nile Red, have become a popular objective criterion to identify small microplastics. Nile Red stains lipophilic particles and confers fluorescence under specific excitation wavelengths. However, Nile Red can stain natural particles and requires a precise sample preparation which may vary between matrices. This preparation is often based on organic matter removal using H2O2, for eliminating plant tissues, or KOH, for animal tissues. Observation can be made directly or under a microscope illuminated by a 470 nm light, ideally emitting ≥1600 lux, and observed through an orange filter. Quantification should be made rapidly due to the risk of losing fluorescence and particles, with an average loss of 74% under 2 months. Despite the convenience of Nile Red, namely cheap and fast quantification of microplastics, it does not provide chemical characterization. In this case, spectroscopy methods capable of identifying particles down to a few µm are required, such as micro-Raman spectroscopy. These methods also require sample preparation to reduce interference and improve throughput. It is recommended that at least some particles should be characterized by spectroscopy, such as by characterizing all particles within 1 mm2 squares in the filter. However, these methods are also limited by a high cost, low availability, and low throughput. Therefore, a combination of identification methods is required for the quantification and characterization of microplastics to allow higher throughputs and the detection of smaller particles.