To determine effects of different fertilizer sources on the yield and quality parameters of Moldavian balm (MB) in intercropping with Fenugreek (FG), two factors were analyzed. The first one included three cropping patterns: MB pure stand, FG pure stand, and intercropping of two rows of MB with two rows of FG (2FG:2MB); the second factor was fertilizer sources: control plants, 100% chemical fertilizer (NPK), 100% bacterial biofertilizers + 25% synthetic fertilizer (BF+25NPK), 75% humic acid (HA)+ 25% synthetic fertilizer (75HA+25NPK), and 75% vermicompost (V)+ 25% synthetic fertilizer (75V+25NPK). Results showed that the highest basic microbial respiration , substrate induced respiration and microbial biomass carbon was observed in intercropping of 2FG:2MB fertilized with 75V+25NPK. This treatment also increased the seed yield of FG and dry matter yield of MB by 54% and 80%, respectively, and resulted in the maximum essential oil (EO) content of MB (0.77%) and oil content of FG (14.2%). In addition, the intercrop of 2FG:2MB fertilized with 75V+25NPK improved the EO quality of MB plants by increasing its geranyl acetate and geranial concentration, and also improved the oil quality in FG by maximizing its unsaturated fatty acids content such as oleic and linoleic acids. Overall, we conclude that intercropping of 2MB:2FG fertilized with a fertilizer mix composed of vermicompost (75%) and synthetic NPK fertilizer (25%) can be suggested to farmers as an eco-friendly and sustainable system practice for improving EO and oil content as well as quality of FG and MB plants, respectively.