Recently, several studies have introduced nanotechnology into the area of dental materials with the aim of improving their properties. The objective of this study is to determine the antibacterial and mechanical properties of type I glass ionomers reinforced with halloysite nanotubes modified with 2% chlorhexidine at concentrations of 5% and 10% relative to the total weight of the powder used to construct each sample. Regarding antibacterial effect, 200 samples were established and distributed into four experimental groups and six control groups (4 +ve and 2 −ve), with 20 samples each. The mechanical properties were evaluated in 270 samples, assessing microhardness (30 samples), compressive strength (120 samples), and setting time (120 samples). The groups were characterized by scanning electron microscopy and Fourier transform infrared spectroscopy, and the antibacterial activity of the ionomers was evaluated on Streptococcus mutans for 24 h. The control and positive control groups showed no antibacterial effect, while the experimental group with 5% concentration showed a zone of growth inhibition between 11.35 mm and 11.45 mm, and the group with 10% concentration showed a zone of growth inhibition between 12.50 mm and 13.20 mm. Statistical differences were observed between the experimental groups with 5% and 10% nanotubes. Regarding the mechanical properties, microhardness, and setting time, no statistical difference was found when compared with control groups, while compressive strength showed higher significant values, with ionomers modified with 10% concentration of nanotubes resulting in better compressive strength values. The incorporation of nanotubes at concentrations of 5% and 10% effectively inhibited the presence of S. mutans, particularly when the dose–response relationship was taken into account, with the advantage of maintaining and improving their mechanical properties.