Land desertification is recognized as a major threat to soil resources in arid, semi-arid Mediterranean areas. The use of widely applicable methodologies can facilitate the identification of land desertification risk spatio-temporal trends, which allows transnational comparison and support the development of soil management practices and policies, protecting the valuable soil resources. The aim of this study is to improve and use the Environmentally Sensitive Areas (ESAs) MEDALUS methodology, in order to provide a qualitative assessment for desertification risk trends in Greece, within the last 45 years. The Management, Vegetation, Soil and Climate quality indices (MQI, VQI, SQI, CQI) and the sub-sequent Environmental Sensitive Areas Index (ESAI) have been modeled for three periods in the entire Greek territory. The four quality indices are divided in two main categories, based on data availability and inherent characteristics, such as the pace of change during the studied period. Particular emphasis is given to the assessment of MQI, by integrating criteria which derived from national policies and the elaboration of national statistical data. The results show about 9% increase of the areas characterized as Critical to land desertification risk, while Fragile, Potentially affected and Non-affected areas decrease by 3.7%, 3.6%, 2.5% respectively. The applied approach for MQI can reveal areas where particular attention to management practices is required and improves the performance of the overall desertification risk index.