In arid and semi-arid regions, intercropping systems combined with biofertilizer application help improve the quantity and quality of food and industrial crops. This study assessed the effect of biofertilizers on the seed yield, essential oil (EO) concentration, fatty acid profile, and phenolic compounds of dragon's head in intercropping patterns under rainfed conditions during the 2019 and 2020 growing seasons. The treatments comprised five planting patterns [sole cropping of dragon's head (D) and chickpea (Ch) and intercropping patterns of 1D:1Ch, 2D:1Ch, 1D:2Ch] and three fertilizer sources [arbuscular mycorrhizal fungi (AMF), bacterial biofertilizers (BI), no fertilization (control)]. The most sustainable combination was 2D:1Ch with BI fertilization, with the highest EO concentration in dragon's head aerial parts (0.94%) and seeds (0.59%). The major EO constituents of dragon's head aerial parts were germacrene-D and (E)-caryophyllene and seeds were 1,8-cineole and O-cymene. The 2D:1Ch intercropping pattern with BI fertilization also had the highest concentrations of linoleic acid, oleic acid, and phenolic compounds (quercetin and chlorogenic acid) and the highest land equivalent ratio (1.15). These results indicate that intercropping and BI fertilization can improve dragon's head cultivation, rendering it a sustainable strategy for EO production under rainfed conditions.