Cultivated plants in the area of the Botanic Garden of P. J. Šafárik University are endangered by a wide range of harmful factors. In greenhouses, it is mainly harmful insects and mites, partly fungal pathogens, in the outdoor area these include mainly unwanted vegetation, wild even-toed ungulates, and occasionally some harmful invertebrates. Due to the effort to minimise the burden on the environment, there is an effort to employ the most environmentally friendly methods (nature-friendly procedures) in the control of these pests and pathogens. To a limited extent and in certain places, albeit necessary, they are still conventional pesticides, but otherwise mechanical and biological agents are preferred within the framework of the Integrated Plant Protection procedures. The year 2006 was a significant milestone in the history of this Botanic Garden, when the programme of biological protection in greenhouses began. Since then, almost all the greenhouses for visitors (except for the greenhouse with succulents) are in the regime of biological protection and traditional pesticides have not been used in these areas since then. This creates a healthier environment for visitors and employees, intentionally bred animals (fish, exotic butterflies) are not endangered and the relevant greenhouses are still accessible without restrictions, which in the past were related to chemical interventions. We are the only Botanic Garden in Slovakia that uses useful predatory and parasitic species of insects, mites and other animals to such an extent, including entomopathogenic fungi and bacteria. Thanks to the applied biological protection, visitors may also see the practical use of knowledge on the relationships between plants, phytophagous and their natural enemies. In practice, we try to present this ecology to the public also through information boards.