Every year there are changes in the register of fungicides available for forestry. It is proactive to develop a new strategy to minimise the application of chemical methods and replace them with natural and biological fungal control options. This study compares the influence after one growing season in a bare-root forest nursery of (a) effective microorganisms (EM) consisting of mixed cultures of beneficial and naturally-occurring microorganisms, (b) the organic fertilizer Actifos (Act), and (c) the mineral fertilizer Busz Forte (BF) on the growth and mycorrhizal colonization of two common forest deciduous tree species: Fagus sylvatica and Quercus robur. None of the analysed growth parameters (root collar diameter, length of shoots and roots, dry mass of shoots, and roots) of either tested tree species differed significantly among treatments. For both tree species, seedlings treated with EM exhibited partnerships with a smaller species richness of mycorrhizae than did seedlings in other treatments. Moreover, EM treatment significantly increased the abundance of non-vital root tips for both species. By contrast, BF exerted a negative effect on F. sylvatica non-vital mycorrhiza abundance. Based on morphological and molecular identification, a total of 11 ectomycorrhizal (ECM) fungal taxa were detected in this study; three species (Peziza ostracoderma, Scleroderma areolatum and Cenococcum-like) were shared between both plant species. Across treatments, the most abundant ECM fungal species on F. sylvatica roots were Pezizaceae sp. (51.1%) and Hebeloma sp. (38.1%), while Peziza ostracoderma (26.8%), Naucoria salicis (24.1%), and Scleroderma areolatum (16.9%) were the most abundant taxa on Q. robur seedling roots. Our data indicate a negative effect of EM on ectomycorrhizal colonisation and on species richness of ECM fungi associated with F. sylvatica and Q. robur seedlings. None of the tested products had a negative effect on seedling growth, but seedlings treated with EM were characterised by a significant higher abundance of non-vital mycorrhizae.