The aim of the review is to describe a control of pests by microorganisms and its possible effect on bees, other pollinators and beekeeping. Biological control seems to be a natural way to solve the problem with pests in agriculture as an alternative to the use of pesticides. However, the proposed solution must be closely associated with the safety to pollinators, which are an important part of plant production as well as forest ecosystems. Entomopathogenic bacteria (mainly bacilli) and entomopathogenic fungi (e.g., Beauveria bassiana and Metarhizium anisopliae) are often used to suppress the pests in agriculture. The application of entomopathogenic microsporidia is controversial because their frequent representatives are pollinators' pests. Moreover, biocontrol can be applied in the form of pollinator strips near the fields with monocultures resulting in plant and pollinator protection. In some countries, bees are also used as biovectors of control agents for the plant protection in the fields. On the other hand, specific pests pose a threat to bees themselves in the hives. Varoosis is a problem in beekeeping all over the world. The suppression of bee pests using microorganisms was tested. An activity of Beauveria bassiana against Varroa destructor shows promising results. Surprisingly, Beauveria bassiana can be isolated from cadavers of Galleria mellonella larvae, another bee pest, which destroy wax combs. Therefore, understanding of various links between the organisms could be helpful for sustainable beekeeping. Overall, humans are more conscious that everything is connected to each other. Protecting agents designed on natural basis often possess excellent results in practice. Therefore, testing them is more than desirable.