<p>Eggshell powder (EP) has been suggested as a cost-effective pulpotomy material due to its high biocompatibility, remineralization potential, and ability to induce dentin bridge formation. This study compared the clinical and radiographic outcomes of EP, Biodentine, and mineral trioxide aggregate (MTA) when used as pulpotomy agents in primary molars. A randomized split-mouth clinical trial was performed on 30 children, each receiving pulpotomy in 3 primary molars assigned to Group I (EP), Group II (Biodentine), and Group III (MTA), with 30 teeth per group. Clinical evaluations were carried out at baseline, 3-, 6-, and 12-month. Cone-beam computed tomography (CBCT) scans were performed immediately postoperatively and at 12- month to evaluate root resorption and radiodensity changes. All groups demonstrated 100% clinical success within 3-month. At 12-month, Group I showed significantly higher rates of spontaneous pain, abnormal mobility, fistula, and internal and external root resorption (<i>p</i> &lt; .05). CBCT analysis revealed significantly lower radiodensity values in Group I compared with Groups II and III. Group III (MTA) exhibited the most favorable radiographic outcomes, followed by Group II (Biodentine). EP achieved acceptable short-term results; however, its long-term performance was inferior to MTA and Biodentine.</p><p><i>Clinical significance</i> EP represents a low-cost, biocompatible, and environmentally sustainable biomaterial derived from recycled natural waste. Despite its eco-friendly and biomimetic advantages, its long-term clinical and radiographic performance remained inferior to Biodentine and MTA, which continue to be the more reliable pulpotomy materials for primary molars.</p><p><i>Trial registration</i> NCT05812053, “ComparativeEvaluation of Eggshell Powder in Primary Teeth Pulpotomy”,<a href="https://clinicaltrials.gov/">https://clinicaltrials.gov/</a>. Registered: 2023/04/13.</p>