The adequate intake of selenium (Se) has great importance for human health. Because Se is incorporated into the food chain through the absorption of crops from the soil, soils deficient in this element ultimately cause deficiencies in livestock and humans. Therefore, those regions/countries with poor soils in Se its population have the risk of developing certain diseases (clinical and subclinical deficiencies). The agronomic Se biofortification (Se-fertilization) of wheat has proven to be an efficient practice for correcting such deficiencies. However, the initial Se levels and their annual variability must be evaluated under specific environmental and crop conditions. The objective of this work was to evaluate the Se content in wheat grain and its temporal variability.Wheat grain samples collected over 16 years for a long-term experiment in southern Spain (Mediterranean climate) in an arid Vertisol, including two tillage systems (conventional and no tillage), were analysed (ICP-MS). The concentrations of Se in grain were very low and highly variable across all years studied, with an overall mean of 28.0 ± 7.5 μg Se kg−1. The wheat yields (3585 ± 1211 kg ha−1) and rainfall (551 ± 200 mm) were also highly variable but were not correlated with Se concentration. The no tillage system did not present differences in the grain concentrations and accumulations of Se compared with those of the conventional tillage system. The total Se in the soil (159.3 ± 15.5 μg Se kg−1) was very low, and Se phytoavailability did not exceed ≤ 1% of the total Se (soil pH 7.7, ≥ 70% clay).The influence of climate on the uptake of Se by wheat grain is complex and is not affected by the tillage system. Therefore, in rainfed Vertisols under Mediterranean climate conditions, the use of Se-biofortification strategies should be analysed in more deep and over a longer study period than used in temperate climate.