The massive application of chemical fertilizers to support crop production has resulted in soil, water, and air pollution at a global scale. In the same time, this situation escalated consumers' concerns regarding quality and safety of food production which, due to increase of fertilizer prices, have provoked corresponding price increase of food products. It is widely accepted that the only solution is to boost exploitation of plant-beneficial microorganisms which in conditions of undisturbed soils play a key role in increasing the availability of minerals that otherwise are inaccessible to plants. This review paper is focused on the employment of microbial inoculants and their production and formulation. Special attention is given to biotechniques that are not fully exploited as tools for biofertilizer manufacturing such as microbial co-cultivation and co-immobilization. Another emerging area includes biotechnological production and combined usage of microorganisms/active natural compounds (biostimulants) such as plant extracts and exudates, compost extracts, and products like strigolactones, which improve not only plant growth and development but also plant-microbial interactions. The most important potential and novel strategies in this field are presented as well as the tendencies that will be developed in the near future.