Flavan-3-ols and their oligomeric forms called proanthocyanidins are polyphenolic compounds occurring in several foodstuffs and in many medicinal herbs. Their consumption is associated with numerous health benefits. They exhibit antioxidant, anti-inflammatory, cytoprotective, as well as antimicrobial activity. The latter property is important in the prevention and treatment of periodontal diseases. Periodontitis is a multifactorial polymicrobial infection characterized by a destructive inflammatory process affecting the periodontium. Using non-toxic and efficient natural products such as flavanol derivatives can significantly contribute to alleviating periodontitis symptoms and preventing the disease’s progress. Therefore, a comprehensive systematic review of proanthocyanidins and flavan-3-ols in the prevention and treatment of periodontitis was performed. The present paper reviews the direct antibacterial effects of these compounds against periodontic pathogens. The immunomodulatory effects, including animal and clinical studies, are included in a separate, parallel article. There is significant evidence supporting the importance of the antibacterial action exerted by proanthocyanidins from edible fruits, tea, and medicinal herbs in the inhibition of periodontitis-causing pathogens.