Origanum dictamnus L. (Lamiaceae) is a perennial herb endemic to the Greek island of Crete, widely used for tea preparation, medicinal purposes, and food flavoring, as well as an ornamental plant. The aim of this work was to introduce the species to the green roof sector while serving urban agriculture. Thus, its growth potential was investigated, along with the content of nutrients (N, P, K, Na) and the accumulation of heavy metals (Cu, Pb, Ni, Mn, Zn, Fe) in its tissues, in two cultivation sites in Athens, Greece, i.e., an extensive green roof and at ground level next to a moderate traffic road. Cultivation took place in plastic containers with a green roof infrastructure fitted, in two substrate types (grape marc compost, perlite, and pumice 3:3:4 v/v, and grape marc compost, perlite, pumice, and soil 3:3:2:2 v/v), with 10 cm depth. Plant growth was favored by the soil substrate, but it was also satisfactory in the soilless one. Cultivation site affected heavy metal accumulation, resulting in higher concentrations both in leaves and in flowers at street level, while no differences were observed in roots. Washing the tissues reduced heavy metal concentrations only in leaves produced at the street level. Substrate type significantly affected Mn concentration in all plant tissues and Fe in roots, with the highest values measured in the soil substrate. Thus, O. dictamnus could be effectively cultivated in sustainable green roofs, better on a soilless substrate to lower construction weight. Careful selection of the cultivation site could minimize contamination with environmental pollutants if human consumption is also desired.