The aim of this study was to investigate the impact of different cultivation systems (soil cultivation, hydroponic cultivation in greenhouse conditions, and hydroponic vertical cultivation in plant factory under different LED lights) and foliar spraying of nano calcium carbonate on pennyroyal plants. Nano calcium carbonate was applied to the plants at a 7-day interval, three times, one month after planting. Results showed that the greenhouse cultivation system with calcium carbonate foliar spraying produced the highest amount of shoot and root fresh mass in plants. Additionally, foliar spraying of calcium carbonate increased internode length and leaf area in various cultivation systems. Comparing the effects of different light spectrums revealed that red light increased internode length while decreasing leaf length, leaf area, and plant carotenoids. Blue light, on the other hand, increased the leaf area and root length of the plants. The hydroponic greenhouse cultivation system produced plants with the highest levels of chlorophyll, carotenoids, and phenolic compounds. White light-treated plants had less iron and calcium than those exposed to other light spectrums. In conclusion, pennyroyal plants grown in greenhouses or fields had better growth than those grown in plant factories under different light spectrums. Furthermore, the calcium foliar application improved the physiological and biochemical properties of the plants in all the studied systems.