The lack of standardized methods to study soil organisms prevents comparisons across data sets and the development of new global and regional experiments and assessments. Moreover, standardized methods are needed to evaluate the impact of anthropogenic stressors, such as chemicals, on soil organism communities in the regulatory context. The goal of this contribution is to summarize current methodological approaches to measure structural and functional diversity of soil organisms, and to identify gaps and methodological improvements so as to cross data sets generated worldwide. This is urgently needed because several currently ongoing regional and global soil biodiversity studies are not coordinated with one another in terms of methodology, including database development. Therefore, we evaluated the standard methods to sample, identify, determine, and assess soil organisms currently applied or proposed, using well-accepted criteria such as ecological relevance; practicability of usage in terms of resources, time, and costs; and the level of standardization. Methods addressing both the structure and the functions of soil organisms (populations or communities) are included, with a special focus on new molecular methods based on nucleic acid extraction and further analyses by polymerase chain reaction (PCR)-based approaches for microorganisms and invertebrates. We particularly highlight the activities of the Technical Committee (TC) 190 of the International Organization for Standardization (ISO) because ISO guidelines are legally accredited by many national or international authorities when they put conservation laws and regulations into practice. Finally, we propose detailed recommendations regarding gaps in the available set of standards, in order to identify a list of new methods to be standardized. We propose to organize this whole process under the Global Soil Biodiversity Initiative (GSBI) in order to ensure a truly global approach for the assessment of soil biodiversity. Integr Environ Assess Manag 2018;14:463-479. © 2018 SETAC. © 2018 SETAC.