Introduction: Root biomodification in periodontal therapy aims at removing the smear layer and enhances the clot stability necessary for periodontal regeneration. Citric Acid (CA), EDTA, fibronectin has been used routinely. But if used injudiciously acidic erosion of the periodontal tissues might occur. Apple Cider Vinegar (ACV) an organic acetic has been reported to possess antimicrobial, anti-inflammatory and antioxidant effects. Aim: To assess the effect of smear layer removal and fibrin clot adhesion of ACV in comparison to CA on periodontally affected teeth. Materials and Methods: This pilot study was conducted at Sri Venkateswara Dental College and Hospital, Chennai, India, for three months, starting in January 2024 and ending in March 2024. 8 Teeth extracted due to periodontal reasons were cleaned, scaled and root planed. From the extracted teeth 16 dentin block samples were obtained, of which eight underwent CA testing (Control group) and eight underwent ACV testing (test group). The SEM analysis was done to assess the efficiency of smear layer removal and fibrin clot adhesion. Results: Under qualitative Scanning Electron Microscope (SEM) analysis, though ACV (50%) and CA (50%) group exhibited significant level of smear layer removal, complete dentinal tubule opening (RMSI score 2) was observed only in ACV category. In regard to Blood Element Adhesion Index (BEAI) both the groups demonstrated moderate fibrin clot adhesion (BEA score 2) in 50% of their samples. Considering both the parameters, root conditioning effects of ACV was better than CA. Conclusion: Teeth treated with ACV had a comparable effect as the CA in terms of root biomodification. This novel agent with several medicinal effects can be considered for future studies to determine its regenerative effectiveness.