In Portugal, many abandoned mines are often close to agricultural areas and might be used for plant food cultivation. Soils in the vicinity of two Mn- and Fe-abandoned mines (Ferragudo and Rosalgar, SW of Portugal) were collected to cultivate two different food species (Brassica rapa subsp. pekinensis (Lour.) Hanelt and Origanum vulgare L.). Chemical characterization of the soil–plant system and potential risk of adverse effects for human health posed by plants associated with soil contamination, based on the estimation of hazard quotient (HQ), were assessed in a microcosm assay under greenhouse conditions. In both soils, the average total concentrations of Fe and Mn were above the normal values for soils in the region and their concentration in shoots of both species was very high. Brassica rapa subsp. pekinensis grew better in Ferragudo than in Rosalgar soils, and it behaved as an excluder of Cu, Mn, Fe, S and Zn in both soils. The HQ for Cu, Fe, Mn and Zn in the studied species grown on both soils was lower than unit indicating that its consumption is safe. The high Mn tolerance found in both species might be due in part to the high contents of Fe in the soil available fraction that might contribute to an antagonism effect in the uptake and translocation of Mn. The obtained results emphasize the need of further studies with different food crops before cultivation in the studied soils to assess health risks associated with high metal intake.