Typical soils in Greece are neutral or alkaline and frequently are lime-rich, conditions that favour the accumulation of trace elements. The traditional use of metal-based fungicides in orchards and vineyards may have led to the accumulation of trace metals. Concentrations of Fe, Cu, Mn, Zn (aqua regia digestion) and some other soil parameters were measured in organically and conventionally cultivated soils (0–30 cm) from vineyards, olive groves and citrus groves of varying ages, and in uncultivated soils. Many vineyards and olive groves are situated in hilly or mountainous areas with sloping ground or terraces in contrast to citrus, which is cultivated in lower lying areas. Due to the difficulty of access, these crops often are cultivated extensively in both systems. Trace metal concentrations were found to lie within the ranges expected for the predominant soil types. Cu concentrations were relatively high (>100 mg kg−1) in a few samples, but were not correlated with the age of the cultivation. A two-way ANOVA analysis showed larger differences in the mean concentrations of Cu, Mn and Zn between different crops (p ≤ 0.001 for Cu, p ≤ 0.05 for Zn, and p ≤ 0.1 for Mn) than between different cultivation systems (no significant differences). The crop by cultivation interaction was not statistically significant for any metal (p > 0.8). Strong correlations (p ≤ 0.001) were found between Fe, Mn and Zn and both clay concentration and CEC, although these relationships were not uniform throughout the different crop and cultivation systems. Concentrations of Cu were related to clay concentrations only for vineyards and to CEC only for citrus. Correlations were not found with organic matter or pH.