Healthy soils are essential for food production, carbon and water storage and buffering climatic change. As the majority of soils are currently considered unhealthy, evaluation of restoration and management practices requires the regular and systematic monitoring of the physical, chemical, and biological conditions of soil and their overall status. To implement this practice, it is essential to have standardized methods to measure a comprehensive set of physical, chemical and biological indicators, alongside conventional soil descriptions. Here, we present a harmonised protocol for the planning of systematic soil monitoring across continental scales at a single timepoint, from site selection, sampling to data generation. This approach will allow for data integration and produce informative outputs for stakeholders, researchers, landowners and policymakers. Our proposed sampling and processing techniques will minimise methodological and sampling bias by monitoring soils with particular focus on soil faunal and microbial biodiversity. These are evaluated against existing methodologies, data resources, and monitoring efforts. The proposed methodology is based on national and European soil research approaches and has been successfully applied in the HORIZON 2020 Soil Missions funded project “Soil Biodiversity into Ecosystem Services” (SOB4ES) that is developing cost-effective biotic and abiotic indicators of soil conditions across land-use types, intensities and pedoclimatic zones covering 12 European nations. Standardised soil monitoring protocols that combine a comprehensive set of soil parameters with total soil biodiversity across the trophic web are key to gathering datasets comparable across a range of ecosystem types. This will enable robust evaluation of soil condition in respect to management practices, environmental policy, and responses to natural and human-induced environmental change.