This study evaluates the effects of intercropping patterns, plant growth‐promoting rhizobacteria and arbuscular mycorrhizal fungi (AMF) on seed yield and yield components of black cumin (Nigella sativa L.) and fenugreek (Trigonella foenum‐graecum L.), as well as the essential oil and fatty acid profile of black cumin. A two‐year two‐factorial field experiment was conducted in 2015 and 2016 to investigate intercropping of black cumin and fenugreek in five ratios and biofertilizer application as AMF and bacteria. Intercropping reveals higher concentrations of nitrogen and phosphorus compared with monocropping, whereas monocropping inoculated with bacteria shows the highest seed yield of both fenugreek (151 g m−2) and black cumin (148 g m−2). Regarding the quality of black cumin, the combination of a black cumin:fenugreek‐intercropping pattern of 66:34 with bacteria fertilization is most promising, as it shows i) the maximum essential oil content, oil yield, and fixed oil content, ii) the highest contents of thymol and p‐cymene, iii) the highest content of linoleic acid, and iv) the maximum land equivalent ratio. Conclusively, bacteria fertilization and black cumin:fenugreek‐intercropping pattern of 66:34 helps improving essential oil, fixed oil quality, and quantity of black cumin, thus creating a more sustainable cultivation system for black cumin and fenugreek.