Due to its excellent properties such as biocompatibility, biodegradability, antibacterial, and antimicrobial effects, chitosan (CHT) demonstrates wide application in the food, agricultural, and pharmaceutical industries, as well as in medicine. The aim of this study was to investigate the antibacterial properties of the prepared porous chitosan-copper (II)/hydroxyapatite-based (CHT-Cu/HAp) scaffolds on Gram-positive (Staphylococcus aureus) and Gram-negative bacteria (Klebsiella pneumoniae). CHT-Cu/HAp hydrogels with varying amount of hydroxyapatite (0, 5, 10, and 20 wt.%) were obtained by neutralisation with 1.25 mol dm^-3 sodium hydroxide solution, while dry porous carriers (aerogels) were obtained through lyophilization. The dry porous CHT-Cu/HAp samples were analysed by Fourier-transform infrared spectroscopy (FTIR), and the results indicate the presence of interactions between the polymer matrix and the filler. The swelling degree (SB) was investigated in phosphate-buffered saline solution (PBS) under physiological conditions (pH 7.4; 37 °C) for 24 hours, and there were no significant statistical differences between samples with different chemical composition, with the swelling degree for all samples ranging between 17–21. The antibacterial properties of the prepared porous CHT-Cu/HAp scaffolds were examined using the disk diffusion method on two bacterial cultures: Staphylococcus aureus (Gram-positive bacteria) and Klebsiella pneumoniae (Gram-negative bacteria). The results show that the samples with the addition of hydroxyapatite (CHT-Cu/HAp5, CHT-Cu/HAp10 i CHT-Cu/HAp20), pre-swollen in PBS for 3 and 24 h, exhibited antibacterial activity against the Gram-positive bacteria. All CHT-Cu/HAp samples show no antibacterial activity against the Gram-negative bacteria. Additionally, all dry samples showed a lack of antibacterial activity against both Gram-positive and Gram-negative bacteria. The successfully prepared porous scaffolds based on chitosan, copper (II) ions, and hydroxyapatite demonstrated good antibacterial properties against Gram-positive bacteria, with potential applications in biomedical field.