Introduction Microorganisms are pivotal contributors to pulp and periapical pathology, often culminating in endodontic treatment failures. The successful outcome of such treatment hinges on the effective eradication of microbial flora through various interventions, including intracanal medicaments (ICMs). However, Enterococcus faecalis (E. faecalis), a highly adaptive Gram-positive bacterium, exhibits remarkable resilience and can persist even after rigorous disinfection efforts. This study explores the efficacy of two ICMs, calcium hydroxide-based triple antibiotic paste (TAP) and a novel alternative containing bromelain, derived from pineapples, in combating E. faecalis infections in vivo. Methodology This in-vivo study was conducted at Sharad Pawar Dental College and Hospital, Wardha, India, and ethical approval was obtained from the institutional ethical committee. The sample size was calculated using the OpenEpi program (version 3.04.04, Open Source Epidemiologic Statistics for Public Health, www.OpenEpi.com), resulting in 15 participants per group. Inclusion criteria encompassed mandibular premolars with carious involvement but no prior restorations, diagnosed with necrotic or infected pulp, and no significant medical history. Exclusion criteria included systemic conditions, pregnancy, retreatment cases, recent antibiotic therapy, calcified canals, and other contraindications. After proper patient consent, access opening and chemomechanical preparation were performed, and root canals (RCs) were randomly divided into two groups: TAP and bromelain paste (BP). TAP was prepared using ciprofloxacin, metronidazole, and minocycline, while BP comprised bromelain powder mixed with saline. Both groups received intracanal medicaments, followed by temporary sealing. Microbiological samples were collected before and after treatment for analysis. Results E. faecalis count (CFU/mL) before instrumentation for the TAP group was (1.94 x 105 [Formula: see text] 7.45 x 103) and for BP group was (1.97 x 105 [Formula: see text] 7.70 x 103) with p-value 0.26 [Formula: see text] p=0.05, so no significant difference was found between them. E. faecalis count (CFU/mL) after instrumentation for the TAP group was (7.70 x 103 [Formula: see text] 9.11 x 102) and for the BP group was (7.26 x 103 [Formula: see text] 8.43 x 102) with p-value 0.18 [Formula: see text] p=0.05, so no significant difference was found between them. However, the E. faecalis count obtained after seven days of intracanal medicament for the TAP group was (3.63 x 101 [Formula: see text] 5.60) and for the BP group was (3.13 x 101 [Formula: see text] 4.55) with p-value 0.012 < p=0.05, so a significant difference was found between them. This means that when compared with the TAP group, there was a greater amount of reduction in E. faecalis count (CFU/mL) for the BP group seven days after the placement of intracanal medicament, and this reduction was statistically significant. Conclusion This in-vivo study highlights the potential of BP as a more effective intracanal medicament against E. faecalis when compared to the conventional TAP. Bromelain's selectivity for Gram-positive bacteria and its diverse therapeutic properties make it a promising natural alternative for endodontic treatment. Further research is warranted to optimize bromelain's clinical application and assess its potential to enhance endodontic outcomes, potentially revolutionizing the field of endodontics.