Purpose <p>To evaluate the clinical performance of Class II resin composite restorations in primary molars following pulpotomy and to compare them with Class II composite restorations in non-pulpotomised primary molars over 24&#xa0;months.</p> Methods <p>This prospective within-patient controlled study included healthy children aged 4–8&#xa0;years with at least one primary molar requiring a Class II resin composite restoration with pulpotomy and one without pulpotomy. Restorations were placed under rubber dam isolation using a fifth-generation adhesive and resin composite. NeoMTA® was used for pulpotomies. Clinical evaluation was performed at 12 and 24&#xa0;months by a blinded examiner using modified ‘USPHS criteria’. Cross-sectional comparisons were performed using Chi-square or Fisher’s exact tests, whilst longitudinal changes were analysed using the McNemar–Bowker test (<i>p</i> &lt; 0.05).</p> Results <p>Forty children (80 teeth) were enrolled initially. At 12&#xa0;months, 37 children (74 teeth) were evaluated, whilst 32 children (64 teeth) completed the 24-month recall. Most restorations in both groups remained clinically acceptable throughout the study period. Marginal integrity was significantly lower in pulpotomised teeth at 12&#xa0;months (<i>p</i> = 0.003) and at 24&#xa0;months (<i>p</i> = 0.011). No statistically significant differences were observed for marginal discoloration, surface texture, wear, postoperative sensitivity, or recurrent caries (<i>p</i> &gt; 0.05). Longitudinal analysis demonstrated significant deterioration in marginal integrity over time in the pulpotomy group (<i>p</i> = 0.041).</p> Conclusions <p>Resin composite restorations in primary molars showed acceptable performance in both groups. However, restorations in pulpotomised teeth demonstrated reduced marginal integrity after 24&#xa0;months.</p>