Understanding the soil biogeochemical responses to increasing global warming in the near future is essential for improving our capacity to mitigate the impacts of climate change on highly vulnerable Mediterranean ecosystems. Previous studies have primarily focused on the effects of warming on various biogeochemical processes. However, there is limited knowledge about how the changes in water availability associated to high temperatures can alter the bioavailability and dynamics of soil elements, thereby impacting ecosystem productivity, species composition, and pollution through soil biogeochemical and hydrological processes. In this study, we investigated the effects of long-term nighttime warming on the extractable concentrations of organic carbon (EOC), total nitrogen (ETN), total phosphorus (ETP), and 17 mineral elements (arsenic (As), calcium (Ca), cadmium (Cd), chromium (Cr), copper (Cu), iron (Fe), mercury (Hg), potassium (K), magnesium (Mg), manganese (Mn), molybdenum (Mo), nickel (Ni), lead (Pb), sulfur (S), strontium (Sr), vanadium (V), and zinc (Zn)) through environmental experiments in a semi-arid Mediterranean shrubland. We explored the potential biotic and abiotic mechanisms underlying the seasonal and long-term changes in extractable-mobilizable elemental composition and concentrations. Our findings revealed that prolonged warming led to higher mean annual soil temperature (with an average increase of 0.67 °C from 1999 to 2014), accumulation of soil organic matter (EOC) and extractable concentrations of soil elements (particularly increased ETP and extractable Ca, Mg, Cu, Sr, Mn, and As). These changes were attributed to uniformly higher activities of extracellular soil enzymes and/or lower plant photosynthetic and nutrient uptake capacity linked to more water deficit under warmer conditions. Seasonality unevenly altered element extractable concentrations, with soil microclimate (temperature and water content) and biological (soil microbial and plant) activity being the main drivers of this variability, thus influencing soil element composition. These results suggest significant fluctuations in the extractable concentrations of specific mineral elements in these soils, implying potential future variations in soil element composition as well as the loss of total element concentrations/contents in semi-arid Mediterranean ecosystems due to increasing warming. Therefore, these findings enhance our ability to predict ecosystem management strategies and mitigate the observed negative impacts on plant-soil systems and water quality in the context of climate change.