Background <p>Dental caries in the primary dentition remains a major concern, with Class II cavities in molars posing particular restorative challenges. BEAUTIFIL Flow Plus X, a giomer-based injectable composite, offers esthetic and mechanical benefits with fluoride release and easier placement in children, while EQUIA^® Forte Fil HT, a glass hybrid restorative, provides enhanced strength for stress-bearing areas. Clinical evidence in primary teeth is still limited, and this study aimed to compare their performance in Class II restorations of primary molars to support material selection in pediatric dentistry.</p> Methods <p>A total of 124 primary molars with Class II cavities were randomized with a 1:1 allocation ratio into two groups: Group I received (EQUIA FORTE HT Fil), while Group II received (BEAUTIFIL Flow Plus X F00). Restorations were placed according to manufacturer’s instructions and evaluated for their esthetic, functional, and biological properties using FDI criteria at 3-, 6-, and 12-month intervals. Restorations with total scores of 4 (repair) or 5 (replacement) were recorded as failures. The trial was approved by the Institutional Research Ethical Committee, Faculty of Dentistry, Ain Shams University. Statistical analyses included the Mann-Whitney U test for intergroup and Wilcoxon signed-rank test for intragroup comparisons. The significance level was set at <i>p</i> ≤ 0.05.</p> Results <p>At 12 months, the clinical success rates were 88.3% for Equia Forte HT Fil and 93.4% for BEAUTIFIL Flow Plus X, with no statistically significant difference (<i>p</i> &gt; 0.05). BEAUTIFIL Flow Plus X demonstrated superior esthetic outcomes, with statistically significant advantages in surface luster (<i>p</i> = 0.002) and color match (<i>p</i> &lt; 0.001). Key functional FDI criteria, including fracture and retention as well as marginal adaptation, were comparable between groups, with no statistically significant differences. Biologically, both materials performed comparably with no significant differences and no observed recurrent caries or postoperative sensitivity in either group.</p> Conclusion <p>Both restorative approaches demonstrated acceptable clinical performance in class II cavities of primary molars after 12 months. While functional and biological outcomes were comparable, BEAUTIFIL Flow Plus X provided superior esthetics.</p> Trial registration <p>This RCT was registered at Clinical Trial.gov with registration number (NCT06000085) on the date of 11/8/2023.</p>