Intercropping Moldavian balm with mung bean is an ecological approach for improving resource productivity. A field experiment was conducted over two growing seasons (2018 and 2019) to determine the effect of fertilizer application on yield and essential oil (EO) productivity of Moldavian balm intercropped with mung bean. The experiment had a two‐factor randomized complete block design (RCBD) with three replicates. The first factor comprised of five cropping patterns: Moldavian balm sole crop (MBs), mung bean sole crop (MGs), one row each of Moldavian balm +mung bean (1MB:1MG), two rows each of Moldavian balm +mung bean (2MB:2MG), and three rows of Moldavian balm +two rows of mung bean (3MB:2MG). The second factor comprised four fertilizer sources: no fertilizer application (C, control), 100% chemical fertilizer (NPK), 50% chemical fertilizer +100% bacterial fertilizer (NPK+BF), and 100% bacterial fertilizer +100% mycorrhizal fungi (BF+MF). The sole crop fertilized with NPK+BF produced the highest seed yields for MG (1189 kg/ha) and MB (7027 kg/ha), while 3MB:2MG fertilized with NPK+BF had the highest nutrient contents. Moldavian balm produced the highest EO content and yield in 2MB:2MG fertilized with NPK+BF. The EO of MB mainly comprised geranyl acetate (30–39%), geranial (20–31%), neral (18–24%), and geraniol (3–8%). In addition, the 3MB:2MG intercropping treatment fertilized with NPK+BF had the highest land equivalent ratio (LER = 1.35). We recommend an intercropping ratio of 2MB:2MG fertilized with NPK+BF is recommended as an alternative and eco‐friendly strategy for farmers to improve EO quantity and quality.