In the last years, different biotechnological approaches were developed to reduce the indiscriminate use of chemical fertilizers and pesticides and enhance plant growth and health. The most attractive, safe, and environmentally mild alternatives include those based on plant beneficial microorganisms. After a long period of studies on isolation, selection, and characterisation of plant-beneficial microorganisms, the main lines of research have been oriented to optimising the fermentation processes to produce high-quality and large volumes of biomass/spores and their further formulation. However, further well-structured schemes for improvement of all main steps of the production of bio-formulates should be developed following the ideas based on “healthy soil-healthy plants-healthy humans”.