Purpose The aim of the study was to compare the 36-month clinical performances of a micro-hybride resin based composites (RBC) and a type II resin modified glass ionomer cement (RMGIC) in the treatment of cervical caries lesions. Methods Thirty-three patients (23 females, 10 males) with at least two cervical caries lesions participated in this study. A total of 110 restorations were randomly placed, half using RBC (Spectrum TPH3, Dentsply Sirona) with respective adhesive system (Prime & Bond NT, Dentsply Sirona) the other half using the RMGIC (Riva Light Cure, SDI, Bayswater, Victoria, Australia). Restorations were assessed at baseline, and after 6, 12, 18, 24 and 36 months using modified USPHS criteria. The data were analyzed statistically (p < 0.05). Results Recall rate was 90.91% at 36 months. Of the RBC lesions 84.3% (n = 43) and of the RMGIC restorations 92.2% (n = 47) were fully retained at 36 months. There was no significant difference between two materials in terms of retention and marginal adaptation (p > 0.05). No relation was found between caries activity, cavity dimensions and marginal adaptation (p > 0.05) but RMGIC restorations showed significantly more discoloration than RBC restorations after 36 months (p < 0.001). Conclusions Considering the middle-term outcomes, both materials showed clinically successful performance in the treatment of cervical caries lesions.