Purpose: The purpose of this study was to compare the periodontal health and clinical success of restoring primary molars with a prefabricated stainless steel crown (SSC) or zirconia crown (ZC). Methods: Six- to nine-year-olds with at least two decayed primary molars were included. Teeth were restored with SSCs and ZCs. Intact contralateral primary molars were evaluated as controls. A simplified oral hygiene index (OHI-S), plaque index (PI), gingival index (GI), and clinical success criteria for the crowns were evaluated during follow-up. Friedman and Wilcoxon tests were used for statistical analysis. Results: Fifty-two teeth were evaluated in 13 children for 12 months. The OHI-S levels were not different at the follow-ups. Teeth restored with ZCs showed lower GI and PI scores than those restored with SSCs, even among controls. All SSCs were retained after 12 months, while two of the ZCs decemented. Minor staining in one ZC and a fracture on the surface of another ZC were observed. Conclusions: The gingival health and plaque accumulation performance of zirconia crowns were better than those of stainless steel crowns and controls. SSCs are highly retentive and viable restorative option, although they were associated with a decline in gingival health.