The adsorption of the antiseptic drug chlorhexidine acetate by halloysite was studied. It was shown that the adsorption kinetic curves obeyed a pseudo-second-order reaction equation. The Langmuir and Freundlich models described well the equilibrium adsorption of chlorhexidine acetate by halloysite. The pristine halloysite powder and the loaded clay were characterized using physicochemical methods such as dynamic light scattering, scanning electron microscopy, X-ray diffraction, nitrogen adsorption–desorption, Fourier-transform infrared spectroscopy and thermal analysis. It was found that the halloysite particles were in the form of cylindrical tubes with sizes in the range of 50–1500 nm. Analysis of the X-ray diffraction data showed that the process of chlorhexidine acetate loading did not change the crystal structure of halloysite. The values of the textural parameters of the materials under study were determined using Brunauer–Emmett–Teller, Barrett–Joyner–Halenda and density functional theory methods. The findings indicated that, by filling the pores of halloysite with chlorhexidine acetate, the volume of the pore space and the pore surface area decreased. In addition, it was found from the biological activity tests that halloysite loaded with chlorhexidine acetate demonstrates antimicrobial activity against Escherichia coli M-17 bacteria.