Fungi and other microeukaryotes (e.g., meiofauna) play pivotal roles in terrestrial, freshwater, and marine ecosystems. They contribute to nutrient cycling, decomposition, and food web dynamics (among others), and thereby to numerous ecosystem services. Yet, they are mostly overlooked in biodiversity monitoring programs. To address this oversight we need to i) improve coordination and standardisation of data collection, ii) make use of high-throughput technologies, including ‘omics, iii) establish comprehensive monitoring programs, that encompass a wide range of biomes, taxonomic groups, and spatial scales, iv) enhance data sharing and accessibility, and v) engage with policymakers and other stakeholders to ensure that monitoring efforts are aligned with their needs. One critical step towards these goals will be the development of Essential Biodiversity Variables (EBVs) for Fungi and other microeukaryotes. EBVs are priority variables designed to operationalise how changes in biodiversity across time, space, and biological level are measured and described. They bridge the gap between raw biodiversity data and derived policy-relevant indicators. This workshop aims at bringing together people, spanning a wide range of relevant backgrounds and expertise, to discuss the development and implementation of EBVs for Fungi and other microeukaryotes (180 min). The expected outcomes are i) a White paper on development and implementation of EBVs for Fungi and other microeukaryotes; and ii) the establishment of a novel cross-kingdom network of experts contributing to the development of EBVs for Fungi and other microeukaryotes.