Aim: To compare 24-month pulp health outcomes of partial caries removal (PCR) and total caries removal (TCR) with composite restoration in primary molars. Methods: 48 children aged 3-8 years with at least one molar with a deep carious lesion were included. 120 teeth were randomized to control (TCR; n = 54; 69% class II) and test (PCR; n = 66; 63% class II) groups. Total absence of carious tissue was confirmed using a blunt-tipped probe in the TCR group. For PCR, excavation was stopped when hardened, dried dentin with a leathery consistency was achieved. Pulpotomy was performed in cases of pulp exposure. Results: Pulp exposure occurred in 2 and 27.5% of teeth treated with PCR and TCR, respectively (p < 0.01). The operative time was significantly higher for TCR than PCR. Success rates were 92 and 96% in the PCR and TCR groups, respectively (p = 0.34). The success rate tended to be lower in occlusoproximal (92%) than in occlusal (100%) lesions (p = 0.08). Conclusion: The clinical and radiographic success rates of PCR and TCR in primary teeth with deep carious lesions were high and did not differ significantly, indicating that PCR is a reliable minimally invasive approach in primary teeth and that the retention of carious dentin does not interfere with pulp vitality. Moreover, PCR provided other clinically relevant advantages over TCR, especially lower incidence of pulp exposure and lower operative time.