The study investigated the effects of the modified conventional glass ionomer cement (GIC) incorporated with casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) on biofilm composition of dental caries. Shear bond strength, durability tests, adhesive remnant index (ARI) and scanning electron microscope were used to measure the physical properties. Microhardness and ions release were determined to evaluate anti-demineralization effects; growth of the biofilm and its composition were assessed using MTT assay and Q-PCR assay. All experimental groups exhibited a significant stimulation of ions release, and reduced attenuation of microhardness. Nearly 39% reduction in the bacterial biofilm was observed with 5% CPP-ACP group. The regulation ability is mainly manifested in the inhibition of S. mutans and promotion of S. gordonii. The modified GICs by exhibiting anti-demineralization effects potentially lead to a reduction in the cariogenicity of plaque and can serve as a putative promising remineralization system with both enhanced antimicrobial and remineralization properties.