Introduction Various intracanal medicaments have been used in cases of chronic apical periodontitis for appropriate disinfection of the root canal system to eliminate microbes especially from the inaccessible areas. Calcium hydroxide is the most common intracanal medicament available in various forms, but its effectiveness with or without iodoform using microbial culture is unknown. Therefore, our aim is to compare the antimicrobial efficacy of Calcipex and Metapex in endodontic treatment of teeth presenting with chronic apical periodontitis by assessing the bacterial load reduction. Method and analysis 60 single rooted teeth of patients with diagnosis of chronic apical periodontitis will be selected and the canals debrided chemomechanically. The patients will be randomised into two groups: Calcipex and Metapex. The first sample (S1) for bacterial culture will be taken before placement of intracanal medicament and the second sample (S2) will be taken after 7 days, before final obturation from the canal and sent to lab for culture. Colony-forming unit will be evaluated. Paired t-test will be used to assess difference between antimicrobial efficacies within the group of medicaments. Independent sample t-test will be used to assess antimicrobial efficacies between groups. Level of significance will be kept at 0.05. Ethics and dissemination Approval from Aga Khan University Hospital Ethical review committee is taken. Findings will be reported according to the Standard Protocol Items for Randomised Trials guidelines. Research findings will be disseminated through annual reports, peer-reviewed journals and conferences. Trial registration number NCT04336709.