The use of intracanal medicaments between appointments can serve as an important aid in the sterilization of the root canal system. Calcium hydroxide is commonly used, but it is not completely effective against Enterococcus faecalis. A triple antibiotic paste (TAP) is used but has the problem of tooth discoloration. Double antibiotic paste (DAP) or modified TAP (MTAP) has been suggested to solve this. Chitosan has been used as a vehicle in pharmacology, and it has inherent antibacterial properties too. This study compares the efficacy of DAP and MTAP using chitosan as a vehicle with calcium hydroxide. Sixty single-rooted teeth were taken and decoronated with a length of 13 mm. Biomechanical preparation (BMP) was done with #3 Gates-Glidden (GG) drills, 17% ethylenediaminetetraacetic acid (EDTA), and 5.25% sodium hypochlorite (NaOCl) used for irrigation. These were kept in microcentrifuge tubes with 1 ml brain heart infusion (BHI)broth. Contamination was done with E. faecalis strain for 21 days. DAP and MTAP pastes were prepared and added to the chitosan solution. Groups were divided into 10 each, each medicament with saline or chitosan as the vehicle. The microbial load was measured at the end of two and seven days. The level of significance was kept at p = 0.05. Statistical analysis was done with the Kruskal-Wallis test and analysis of variance (ANOVA). DAP and MTAP groups with chitosan showed a significant reduction in the microbial load when compared to calcium hydroxide with chitosan. DAP and MTAP with chitosan can be effective intracanal medicaments against E. faecalis in refractory endodontic cases.