Isoliquiritigenin (1) and liquiritigenin (2) are structurally related flavonoids found in a variety of plants. The purpose of this study was to perform a comparative analysis of biological properties of these compounds in regard to their therapeutic potential for oral infections. Compound 1 demonstrated significant antibacterial activity against three major periodontopathogens, Porphyromonas gingivalis, Fusobacterium nucleatum, and Prevotella intermedia. In contrast, 2 exerted less pronounced effects on the above bacterial species. Neither compound was effective against cariogenic bacteria (Streptococcus mutans and Streptococcus sobrinus). Furthermore, 1 exhibited a stronger inhibitory activity than 2 toward P. gingivalis collagenase and human matrix metalloproteinase 9. Finally, the capacity of 1 to attenuate the inflammatory response of macrophages induced by Aggregatibacter actinomycetemcomitans lipopolysaccharide (LPS) was much higher when compared to 2. The activation of transcriptional factors nuclear factor-κB (NF-κB) p65 and activator protein-1 (AP-1) associated with the LPS-induced inflammatory response in macrophages was inhibited strongly by 1, but less affected by 2.