Objectives <p>This study aimed to evaluate clinical and biochemical periodontal responses associated with different crown materials used in primary molars.</p> Materials and methods <p>A total of 21 children with full crown indication in primary molars (<i>n</i> = 84) were treated with prefabricated zirconia crowns (PZCs), stainless steel crowns (SSCs), and fiberglass crowns (FGCs) in a split-mouth study design; unrestored teeth were considered as the control group. Matrix metalloproteinase-8 (MMP-8) and interleukin-1β (IL-1β) levels, plaque index (PI), gingival index (GI), bleeding on probing (BOP) and probing pocket depth (PPD) were evaluated at baseline, 3 months, and 6 months. Continuous outcomes were analyzed using robust mixed analysis of variance, whereas ordinal clinical outcomes were evaluated using generalized estimating equations.</p> Results <p>PPD did not significantly differ among the groups. GCF volume, MMP-8, and IL-1β levels showed significant group and time effects. FGCs exhibited significantly higher IL-1β levels compared to the control, SSC, and PZC groups. MMP-8 levels were significantly higher in the FGC group than in the PZC group, and the group × time interaction indicated increasing MMP-8 levels over time in both the FGC and SSC groups. PZCs demonstrated the most favorable clinical periodontal outcomes, with significantly lower PI, GI, and BOP scores than FGCs during follow-up.</p> Conclusions <p>Crown materials were found to affect both clinical periodontal parameters and inflammatory biomarker levels. Among the evaluated materials, PZCs demonstrated the most favorable periodontal profile, whereas FGCs were found to be associated with less favorable clinical and biochemical periodontal outcomes.</p> Clinical relevance <p>Crown material selection may affect periodontal health and should be carefully considered when planning restorative treatment in pediatric patients.</p> Trial registration <p>NCT07611292, 20.05.2026, retrospectively registered.</p>