Bacterial resistance represents a serious problem in modern medicine. It allows bacteria to prosper, despite the presence of antibiotics, leading to increased healthcare costs and, ultimately, mortality. Due to the lack of drugs, as an alternative solution, antimicrobial peptides are being explored for their potential activity against various microorganisms. These peptides, anoplin, and indolicidin, can destabilize bacterial membranes due to their amphipathic character. To enhance therapeutic efficacy and stability, our research is focusing on conjugating peptides with oligonucleotides, which provides more structural stability while allowing precise targeting. This study focuses on the synthesis and analysis of peptide-oligonucleotide conjugates using click chemistry. 14 compounds were synthesized, including conjugates of peptides and oligonucleotides and complexes of different oligonucleotides. The compounds were characterized by UV/Vis and fluorescence spectrophotometry and circular dichroism spectrometry. The synthesis was monitored by gel electrophoresis, and the final products were subjected to microbiological testing. The authenticity of the conjugates and the final products could not be confirmed with structural analysis. Therefore, the products of the click-synthesis and the annealed conjugates should be analysed by mass spectroscopy.