Background: Periapical abscesses, radicular cysts, and periapical granulomas are the most frequently identified pathological lesions in the alveolar bone. Many studies have been conducted to study the associated cellular and immunological aspects. However, the underlying impact of metabolomics-microbial microenvironment in relation to each lesion is not well identified. Objectives: The objective of this study is to correlate the significant unique metabolic profile to the clinical behavior and the in vitro physiological effect in each periapical lesion. Besides, the correlation of the microbial profile and its associated predicted metabolic activities to each lesion was also identified. Methods: The clinical samples from each lesion were separately subjected to metabolite extraction followed by gas chromatography-mass spectrometry analysis. The expression of associated genes was identified using quantitative real-time polymerase chain reaction in combination with bioinformatics analysis. These followed by translational in vitro analysis using Periodontal Ligament Fibroblasts (PdLFs) and Peripheral Blood Mononuclear Cells (PBMCs) to validate the metabolomics data. Fluidigm and next generation sequencing were used for the identification of microbial profile associated with each lesion. Targeted transcriptomics and protein abundance were employed to draw a final predicted model of the pathogenesis mechanism in periapical lesion. Results: Metabolomics analysis identified unique metabolic profiles associated with each lesion compared to healthy control while unique metabolic pattern was positively correlated to the levels of Interleukin (IL-) 8, Matrix Metalloproteinases (MMP)-1, MMP-9, Cytochrome P450 (CYP) 4F3, and Vascular Endothelial Growth Factor (VEGF) α in abscesses, others were significantly participated in lipophagy and apoptosis induction in cysts, or fibrosis and chronic inflammation in granuloma. 16-20-Hydroxyeicosatetraenoic acids, lipophagy, and retinoid X-Vitamin D receptors were the most