The areas under the organic production of medicinal and aromatic plants are constantly increasing, both domestically and globally. Since organic production does not allow the application of synthetic fertilizers, organic fertilizers like compost and bacterial biofuels have special importance. The aim of this paper is to point out the positive effects of the application of these fertilizers in the organic production of medicinal and aromatic plants. Microbiological fertilizers and compost not only have beneficial effects on the productivity of medicinal and aromatic plants by improving physical and biological properties of the soil, but also affect the quality and increase the content of essential oils and also improve the physiological status of a plant. Azotobacter produce anti-fungal compounds that protect against plant pathogens, while increasing germination and vitality of plants demonstrates the importance of their application in the organic production of medicinal and aromatic plants.