Medicinal plants, as important sources of secondary metabolites, are used for treating different diseases. It is accordingly pertinent to find methods, which may improve their growth and quality in different conditions including variable stresses. It was hypothesized micronutrients use and suitable genotypes may improve Satureja growth and quality in drought stress conditions. The objective of this study was to investigate the effects of drought stress (irrigating plants each 3 (A1), 6 (A2) and 9 days (A3)), micronutrients (Mn and Cu at 0 (M1), 20 (M2) and 40 mgL−1 (M3)), and field location (Isfahan (F1) and Golpayegan (cooler) (F2), Isfahan province, Iran) on the biochemical properties of different Satureja species including S. bakhtiarica, S. khuzestanica and S. mutica. The experimental treatments significantly affected the measured parameters including nodule number, essential oil, antioxidant activity, proline, Mn and Cu contents, and relative water content. Although Cu and Mn, enhanced plant biochemical properties, especially in M2, in some cases, the two micronutrients, unfavorably affected plant properties in M3. The responses of genotypes were different in the two research fields and S. bakhtiarica performed better in F2. The highest essential oil was resulted by A2. The two micronutrients improved plant responses in drought stress by increasing nodule number (148 %), and essential oil yield (143 %) and decreasing plant relative water content and conserving plant water. The use of Mn and Cu is recommendable for planting Satureja species in drought stress conditions, as the two nutrients may enhance plant tolerance by increasing proline production and antioxidant activities.