The purpose of this randomized, split-mouth-designed controlled and single-blinded clinical study was to evaluate the 3-year clinical performance of Class I and Class II resin composite restorations placed with or without cavity lining with a flowable composite. Fifty patients with treatment needs in two premolars or molars were included. One of the teeth was restored using the nanohybrid composite (Grandio®SO, control group), in the test group a high viscosity flowable composite was additionally applied as a first layer. In both groups, the same self-etch adhesive system was applied. Clinical evaluation after 3 years was carried out using the modified USPHS/Ryge criteria. At the 3-year follow-up the recall rate was 92%. Four restorations failed in the test group (8.7%), three due to the loss of vitality and one after fracture. The control group exhibited a cumulative success rate of 100%, while the test group achieved a success rate of 91.3%. This led to significant differences in the annual failure rate (AFR) between the two groups, with rates of 0% and 2.9% (p < 0.05; Mann–Whitney U-test). After 3 years the cumulative survival rate including all restorations was 95.7%. Statistical analysis revealed significant differences for the parameters: tooth vitality, marginal discoloration, success rate, and AFR. The other parameters exhibited no significant differences. Consequently, the nanohybrid composite demonstrated excellent performance over a 3-year period, whereas the utilization of a flowable composite for the cavity lining did not appear to exert a beneficial influence on clinical outcomes.