Periodontitis has been linked to systemic inflammation, however research on its role in causing systemic diseases remains limited. Recent studies explore probiotics for microbiome modulation and enhancing natural compound bioavailability. This study investigated periodontitis-related systemic disease mechanisms, and evaluated the mitigation effects of bioconversion product using Lactiplantibacillus plantarum SMFM2016-RK and Artemisia herba-alba extracts. Four types of bioconverted milk [BM1 (L. plantarum SMFM2016-RK), BM2 (BM1 + A. herba-alba ethanol extract), BM3 (BM1 + A. herba-alba hot-water extract), and BM4 (BM1+ both A. herba-alba extracts)] were studied in a periodontitis-induced rat model. Rats were divided into six groups: normal control, skim milk with ligature, and four BM groups with ligature. Periodontitis induction elevated trabecular resorption (0.325 ± 0.057 mm³) and histopathological symptoms. Serum ALT (55.6 ± 6.6 U/L), glucose (261.7 ± 64.3 mg/dL), insulin (1.90 ± 0.87 ng/mL), inflammation in the liver and colon, and gluconeogenesis-related enzyme expression increased. Periodontitis-induced rats showed gut dysbiosis, with decreased Lactobacillaceae level and increased Oscillospiraceae level. BM3 administration significantly reduced the serum glucose (190.9 ± 27.8 mg/dL), ALT (40.5 ± 5.0 U/L), inflammation, and gluconeogenesis-related enzymes, while increasing tight junction proteins expression and phylum Actinobacteria levels in the gut microbiome. The findings highlight the systemic impact of periodontitis on inflammation, glycemic control, and gut microbiome balance. BM3 effectively alleviated these effects suggesting therapeutic potential.