The present experiment describes a synthesis process of composites based on graphene oxide, which was tested as a carrier for composites of metal- or metalloid-based nanoparticles (Cu, Zn, Mn, Ag, AgP, Se) and subsequently examined as an antimicrobial agent for some bacterial strains (Staphylococcus aureus (S. aureus), methicillin-resistant Staphylococcus aureus (MRSA) and Escherichia coli (E. coli). The composites were first applied at a concentration of 300 μM on all types of model organisms and their effect was observed by spectrophotometric analysis, which showed a decrease in absorbance values in comparison with the control, untreated strain. The most pronounced inhibition (87.4%) of S. aureus growth was observed after the application of graphene oxide composite with selenium nanoparticles compared to control. Moreover, the application of the composite with silver and silver phosphate nanoparticles showed the decrease of 68.8% and 56.8%, respectively. For all the tested composites, the observed antimicrobial effect was found in the range of 26% to 87.4%. Interestingly, the effects of the composites with selenium nanoparticles significantly differed in Gram-positive (G+) and Gram-negative (G−) bacteria. The effects of composites on bacterial cultures of S. aureus and MRSA, the representatives of G+ bacteria, increased with increasing concentrations. On the other hand, the effects of the same composites on G− bacteria E. coli was observed only in the highest applied concentration.