Propolis-based therapeutic agents represent this potential for the development of new drugs in dental care. The aim of a clinical-cohort study was to determine the influence of application of toothpaste enriched with Brazilian extract of propolis (EEP) on health status of oral cavity. Laboratory analysis was conducted in order to assess the chemical composition of EEP including total phenolic compounds, the DPPH (1,1-diphenyl-2-picrylhydrazyl) radical scavenging activity, ABTS radical cation scavenging activity, and FRAP assay. Clinical research involved two groups of subjects comprising 32 adult patients, with assessment based on the preliminary evaluation of the state of their marginal periodontium. The investigation of oral health indices API, OHI, and SBI and microbiological examination of oral microflora were also carried out. Results obtained indicated time-dependent microbial action of EEP at 50 mg/L concentration, with antimicrobial activity against Gram-positive bacteria. The total decrease of API, OHI, and SBI mean values was observed. Hygienic preparations with 3% content of Brazilian ethanol extract of green propolis (EEP) efficiently support removal of dental plaque and improve the state of marginal periodontium.