Intercropping is one of the most important components of sustainable agriculture. The effects of chemical fertilizer (CF), arbuscular mycorrhizal fungi (AMF) (Glomussp.) and AMF + nitrogen-fixing bacteria (NFB) includingAzospirillumandAzotobacter(AMF + NFB) was studied on essential oil yield and compositions of Moldavian balm (Mb) (Dracocephalum moldavicaL.) in sole cropping and intercropping with fenugreek (F) (Trigonella foenum-graecumL.). The experiment was conducted during 2020 and 2021 growing seasons in East Azarbayhan, Iran. The highest dry herbage yield (6132 kg ha−1) was obtained in Mb:F(4:2) and CF treatment. After sole Moldavian balm, the highest essential oil yield (15.28 kg ha−1) was obtained in Mb:F (4:2) and AMF + NFB treatment. Geranial, geranyl acetate, geraniol, neral, and nerol were the main chemical constituents of essential oil. In AMF + NFB treatments the geranial contents in intercropping patterns of Mb:F (1:1), (2:2) and (100:50), increased by 25.1, 15.5 and 34.6% compared with sole Moldavian balm. The highest LERTvalues were observed in Mb:F (100:50) cropping pattern in 2021 (1.70 and 1.63 for CF and AMF + NFB treatments). Generally, it can be concluded that Mb:F (100:50) intercropping and use of AMF + NFB bio-fertilizer could be recommended to medicinal plant growers in sustainable production systems.