Contamination of agricultural soils with heavy metals is a growing global concern with an increase in anthropogenic activities. Despite local studies conducted, no accurate and comprehensive results about agricultural soils of Iran entirely and regarding the climate have been observed regarding heavy metal concentration. Therefore, the present study is aimed at determining a reliable heavy metal concentration in agricultural soils and evaluate the effect of climate on the average concentrations. To provide harmonized and comparable data, 711 soil surface samples were randomly taken from all of the agricultural soils of Iran during 2016–2018. Also, to evaluate the effect of climate, samples were divided into three parts according to major climates of studied area. Results revealed that the average concentration of Cd, Cr, Co, Cu, Mn, Ni, Pb, Zn, and V in agricultural soils was 0.31, 101, 27.9, 37.2, 702, 68.0, 28.2, 73.0, and 101 mg/kg, respectively. The concentration of Cr, Ni, Co, V, and Pb in, respectively, 28.4, 11.3, 8.72, 1.60, and 1.34% of soil samples was higher than the national standard in contrast to the concentration of the other element, which was lower. There were no significant differences between the average concentrations of heavy metals in agricultural soils with respect of climate, indicating the minimum effects of soil forming factors on soil heavy metals. Comparing the mean concentration of heavy metals in three major climatic zones of the country, it seems that geochemistry is the key factor controlling the concentration of metals in agricultural soils of Iran.