The Southeastern European territory is under severe climatic pressure owing to accelerating dry-thermal trends. The present survey illustrates the spatial and temporal evolution of the climate regime over the natural and agricultural landcover of South-eastern Europe and individual countries (Albania, Bosnia Herzegovina, Bulgaria, Croatia, Greece, N. Macedonia, Montenegro, Romania, Serbia, and Slovenia). For this purpose, an high spatial resolution of the Johansson Continentality index, Kerner Oceanity index and Pinna Combinative index was estimated for the first time over two climatic periods (1964–1993; 1994–2023). The Johansson index depicts increasing continentality over the southern and eastern regions, majorly by the spatiotemporal expansion of the Continental climate over the agricultural and natural areas of Bulgaria (respectively, from 49.9% to 73.7% and from 13.3% to 36.8%) followed by Serbia, Romania, and Greece. The Kerner index illustrates increasing continentality over most of the study area owing to the spatiotemporal increase of the Sub-Continental climate type over the agricultural and natural areas of Bosnia Herzegovina (from 68.6% to 84% and from 41.4% to 63.2%), N. Macedonia, Slovenia and the natural areas of Croatia and Serbia. The extension of the Continental over the agricultural and natural areas of Romania is also shown. The Pinna index exhibits an increasing aridity trend, which is more intense in the central and eastern regions. This trend is demonstrated by the higher distribution of the Semi-Dry in the second period mostly over the agricultural and natural areas of Bulgaria (2.4% to 23.1% and 0.7% to 5.8%), and a remarkable expansion of the Moderate Wet climate over both area types of Romania (from 3.3% to 44.8% and from 5.6% to 15.2%) and Bosnia Herzegovina (from 13.7% to 33.5% and from 3.5% to 13.2%). This study’s results highlight the necessity for intensifying adaptation plans and actions aiming at the feasibility of agricultural practices and the conservation of natural areas.