<p>Microorganisms with beneficial traits for protection of plants against pest and diseases and for biostimulation of plants have been selected amongst the huge diversity of microorganisms naturally occurring in the environment. The use of microbial products has to be approved by governmental authorities before they can be applied in the EU. Frameworks of regulations have been developed with particular emphasis on risk assessments of the active substances and the formulated products. Distinctly different regulations are currently used for microbial plant protection products and microbial biostimulants. If the intended purpose of use results in different potential risks, a separation into different legal frameworks is adequate. This may be the case if distinct microbial groups used for different purposes differ in toxicity and pathogenicity. A separation may also be adequate if methods and rates of application or targeted environmental compartments differ resulting in different expected risks for humans, animals, plants or the environment. Also the exploitation of different modes of action may result in different levels of risks and urge different ways of risks assessments. Objective of this review is to stimulate discussion on the reasoning of the separated regulatory frameworks and contrasting risk assessments currently applied in the EU for beneficial microorganisms used for plant protection and used for biostimulation of plants.</p>