Plastic pollution is one of the major challenges in the Anthropocene. A plastic waste sub-product, microplastics (<5 mm), has been regarded as contaminants of concern for its detrimental effects and widespread in the environment. Most studies assessing microplastics focused on marine environments, while terrestrial and soil systems have been overlooked. In this review, we analyzed the current knowledge regarding microplastic pollution in natural soil or agricultural ecosystems. We focused on reviewing the procedural steps for microplastic extraction and identification in detail. The heterogeneity of the methods applied, lack of standardized procedures and incompatible parameters reported, make the results incomparable among most studies. Several microplastic concentration units are needed to make studies comparable. Correctly determining and reporting microplastic morphotypes are key to understanding the sources of contamination. Minimal considerations and recommendations were stated for extraction, digestion, filtration, and polymer identification procedures. Baseline contamination prevention measures were identified as mandatory along the entire sampling, handling and identification procedures. Lastly, knowledge gaps were identified and discussed for further research.