Following up on previous reports prepared for the Commission on Genetic Resources for Food and Agriculture, and acknowledging FAO’s long tradition of technical work on the management of microorganisms and invertebrates in food and agriculture, the present paper responds to the need for a detailed assessment of the state of art in the conservation and sustainable use of soil microorganisms and invertebrates. It focuses on microorganisms and invertebrates contributing to nutrient cycling and the removal of contaminants from soils. The study is based on an extensive literature review and summarizes current views on the taxonomy, conservation, use and exchange of soil microorganisms and invertebrates, highlighting knowledge gaps, needs and challenges. In order to encompass the views of a wide range of stakeholders on knowledge gaps and critical issues related to the conservation and sustainable use of these organisms, the Austrian Institute of Technology (AIT) circulated an invitation to complete an open online survey to several hundred researchers, institutions and organizations worldwide. Twenty-seven responses were received and evaluated. AIT also organized an online expert workshop entitled Status and Trends of Conservation of Soil Microorganisms and Invertebrates, with Emphasis on Bioremediation and Nutrient Cycling Organisms. Twenty-six international experts participated in three parallel sessions: (i) nutrient cycling in soil; (ii) bioremediation in food and agriculture systems; and (iii) conservation of microorganisms and invertebrates, practices, policies and needs. The issues raised in the survey responses and at the workshop were taken into account in the drafting of the study.