Soil's vulnerability to soil threats (STs) and its capacity to deliver soil based ecosystem services (SESs) depend on specific environmental conditions. Therefore, STs and SESs require to be assessed using explicit and appropriate methodologies. Indicators are suitable communications tools with stakeholders and the general public because they facilitate the simplification of complex human-environmental systems and provide aggregated information on certain phenomena at the spatial and temporal scale that they represent. Task 2.3 of the SERENA project was aimed at developing harmonised methodologies to evaluate bundles of soil threats (STs) and soil-based ecosystem services (SESs) at different levels. The Deliverable 2.3.1 developed the second step of the harmonization of STs and SESs indicators, whereas this deliverable developed the third step of the global tiered strategy for harmonisation and was mainly focused on the definition of methods for the harmonised assessment of indicators of STs and SESs at the member state (MS) level. The deliverable was focused on soil erosion (ST) and soil erosion control (SES), soil organic carbon (SOC) loss (ST), greenhouse gas (GHG) and climate regulation (SES), and soil sealing (ST) as well as a bundle of STs/SESs. Different cookbooks were developed to provide harmonized approaches/methods for assessing indicators for STs/SESs at national scale. The cookbooks for each indicator of ST/SES (including bundles of STs/SESs) reported in this deliverable were provide to Task 3.2 for their application at MS scale and subsequent validation of these applications by Task 1.3.