This study aims to synthesize and characterize lignin-decorated zinc oxide nanoparticles before incorporating them into resin-modified glass ionomer cement (RMGIC) to improve their anticariogenic potential and mechanical properties (shear bond strength and microhardness). Probe sonication was used to synthesize lignin-decorated zinc oxide nanoparticles which were then characterized via scanning electron microscopy, Fourier transform infrared spectroscopy, and X-ray diffraction. Following characterization, these were incorporated in RMGIC (Gold label, Fuji II LC). Three major groups, experimental group A (EGA), experimental group B (EGB), and control group (CG), were outlined. EGA and EGB were divided into numbered subgroups based on the ascending concentrations of nanoparticles (5, 10, and 15%) of lignin-coated zinc oxide and zinc-oxide, respectively. CG served as a control and comprised cured RMGIC samples without any incorporation. Anticariogenic analysis was conducted on experimental RMGIC samples via disk-diffusion (n = 3) and direct contact test (n = 3) against Streptococcus mutans (ATCC 25175). Optical density values for days 1, 3, and 5 were recorded via a UV− Vis spectrophotometer. A shear bond strength test was performed using 35 premolars. The adhesive remnant index was used to estimate the site of bond failure. For the Vickers microhardness test (n = 3), 100 g of load at 10 s dwell time was set. Atomic absorption spectroscopy was performed over 28 days to determine the release of zinc from the samples. All tests were analyzed statistically. The anticariogenic potential of EGA and EGB was significantly greater (p ≤ 0.05) than that of the control. The shear bond strength test reported the highest value for EGA15 with all groups exhibiting failure at the bracket/RMGIC interface. The microhardness of EGA15 yielded the highest value (p ≤ 0.05). Release kinetics displayed a steady release with EGB15 exhibiting the highest value. The EGA and EGB samples displayed good anticariogenic potential, which was sustained for 28 days without any deleterious effect on the shear bond strength and microhardness.