Central to the EU thematic strategy for soil protection is that areas affected by soil degradation through erosion, soil organic matter (SOM) decline, compaction, salinization and landslides should be identified in a clear and consistent way. However, the current methodologies to achieve this often differ and this can result in different perceptions of risks amongst EU Member States. The aims of this paper are to: (i) assess the current status of assessment methodologies in Europe (EU27) associated with erosion, SOM decline, compaction, salinization and landslides and (ii) discuss the issues associated with harmonization of these methodologies throughout the EU27. The need for harmonization is assessed using the relative share of common elements between different methodologies. The results demonstrate that the need for harmonization in methodology is greatest for erosion and compaction and least for SOM decline and landslides. However, many of the methodologies which were investigated are still incomplete and there are significant differences in terms of: (i) understanding the threats, (ii) methods of data collection, (iii) processing and interpretation and (iv) risk perception. We propose two options for the harmonized assessment of soil threats: (i) a two-tiered approach based on data availability and spatial scale and (ii) a combination of standardization and harmonization for each assessment methodology. Future assessments should focus on the advantages and disadvantages of these options as the current situation will result in endless discussions on differences and the merits of particular methodologies instead of taking appropriate measures to reduce or eliminate the actual threats.