Investigating the toxicity of naturally occurring or synthesized nanoparticles for various applications is absolutely necessary for environmental protection and safety use. The aim of these research was to investigated the phytotoxicity, cytogenotoxicity and antibacterial potential of the extracts with gold-silver bimetallic nanoparticles (Au-Ag NPs) obtained from green synthesis in Asplenium scolopendrium L. and Dryopteris filix-mas (L.) Schott spores extracts. To our knowledge, this is the first report of the Au-Ag NPs phytosynthesis based on extracts obtained from fern spores. UV-Vis spectroscopy analysis of the samples revealed the maximum absorbance, characteristic of samples with bimetallic nanoparticles, which varied depending on the Au:Ag ratio. Energy-dispersive X-ray spectroscopy confirmed the presence and distribution of Au, Ag and other chemical elements. The presence of specific secondary metabolites in the extracts that helped in NPs biosynthesis stimulated growth processes. Good results were recorded for some Dryopteris filix-mas samples, correlated with a significantly increased mitotic index. Cell viability decreased significantly in three of the nanoformulations. Only extracts with Au-Ag NPs showed antimicrobial effect against Staphylococcus aureus ATCC 25923, Bacillus subtilis ATCC 6633 and Escherichia coli ATCC 8739. The testing of the antibacterial potential of these extracts must be extended to other bacterial strains and other microorganisms, the search of new antimicrobial resources being an urgent necessity nowadays.