Aim and objective: To compare the quality or quantity of dentin bridge formation of Biodentine and Propolis with the current gold standard—mineral trioxide aggregate (MTA) when used as a direct pulp-capping agent. Materials and methods: Randomized clinical trial on 102 teeth (patients aged 13–30 years) selected for extraction due to orthodontic treatment was carried out by a single operator using group I—MTA, group II—Biodentine, and group III—Propolis as vital pulp therapy agents. The patients and the outcome assessor were blinded. After 3 months of follow-up, the teeth were extracted and sent for the histopathological analysis. The Chi-square test was applied on the data for statistical analysis. Results: Pulp sensibility was maintained for all assessed teeth after the follow-up period. The difference between group I and group II was statistically insignificant. Group III showed significant differences in terms of morphology, continuity, and thickness when compared to the other two groups (p = 0.0). Conclusion: The three groups successfully aided in forming dentin bridges in all the assessed teeth after follow-up. The quality and quantity of dentin bridge formation of group I—MTA and group II—Biodentine were superior than group III—Propolis. Owing to its anti-inflammatory, antimicrobial, and tissue regeneration properties, Propolis improves wound healing and can be successfully used as an agent in direct pulp capping. Clinical significance: Biodentine is an effective pulp capping agent and is comparable to MTA. Among other advantageous properties, Propolis is an organic anti-inflammatory material that can be successfully used as a direct pulp-capping material due to its ability to induce reparative dentin, which is good enough to maintain pulp sensibility over a long period of time.