Abstract: The human oral microbiome typically contains over 700 different microbial species. How they interact can shape the microenvironment throughout the human body, as these interactions are paramount to maintaining oral and overall systemic health. Previous epidemiological studies have linked dysbiosis of oral microbes with several chronic ailments such as cardiovascular disease, poor glycemic control in diabetics, and rheumatoid arthritis. Recent advances in technology, including next-generation sequencing (NGS), have revealed the complexities of the oral microbiome, but the role of microbial and molecular interactions during systemic disease progression remains poorly understood. Here we show significant shifts in the oral metabolite profile during the progression of early-stage periodontal disease (gingivitis) and identify several key metabolites as quantitative measures for gingivitis progression. In addition, our study reveals a previously unknown metabolic lag in recovery of the normal oral cavity metabolome after the resumption of recommended oral hygiene practices. which suggests the potential for lingering harmful sequelae of gingivitis. This work represents a characterization of the human oral metabolome over 35 days, providing a high-resolution metabolomic landscape for understanding oral health during gingivitis and opening new opportunities for combating progressive periodontal disease.