The aim of this randomized, controlled, single-blind and prospective study was to evaluate the clinical and radiographic success rates of three different bonding protocols vs calcium hydroxide liner for protection of the dentin-pulp complex of primary molars with different remaining dentin thicknesses. Two hundred forty primary molar teeth with moderate to deep occlusal caries were restored in 97 children who met inclusion criteria. After cavity preparation, the teeth were randomly assigned into four groups (n=60/group) with respect to the material used for protection of the dentin-pulp complex: (1) total-etching with 36% phosphoric acid followed by an acetone-based adhesive (Prime&Bond NT), (2) a self-etch adhesive system (Xeno 111), (3) an acetone-based adhesive (Prime&Bond NT) without prior acid conditioning, and (4) control: calcium hydroxide cement (Dycal). Teeth in groups 1-3 were restored with a polyacid-modified resin-based composite (Dyract AP) and those in group 4 with amalgam. The remaining dentin thickness was calculated using image analysis software (ImageJ). The teeth were evaluated clinically and radiographically for 24 months. The distribution of restored teeth with minimal remaining dentin thickness (<= 0.5 mm) was 3.3, 8.3, 8.3, and 10% for groups 1, 2, 3, and 4, respectively. Despite the absence of pulpal protection in groups 1-3, none of those teeth exhibited any significant clinical or radiographic symptom during the study period. After 2 years, the clinical and radiographic success rate of restorative treatments was 100%. Protection of the dentin-pulp complex with the tested bonding protocols resulted in similar outcomes in mainly shallow and medium deep cavities as compared to calcium hydroxide amalgam in more deep cavities, when indirect pulp treatment was performed in class I compomer restorations.