To evaluate the impact of using ion-releasing liners on the 3-year clinical performance of posterior resin composite restorations after selective caries excavation with polymer burs. 20 patients were enrolled in this trial. Each patient had two deep carious lesions, one on each side of the mouth. After selective caries removal using polymer bur (PolyBur P1, Komet, Brasseler GmbH Co. KG, Lemgo, Germany), cavities were lined with bioactive ionic resin composite (Activa Bioactive Base/Liner, Pulpdent, Watertown, MA, USA) or resin-modified glass ionomer liner (Riva Light Cure, SDI, Bayswater, Victoria, Australia). All cavities were then restored with nanofilled resin composite (Filtek Z350XT, 3M Oral Care, St. Paul, MN, USA). All the tested materials were placed according to the manufacturers’ instructions. Clinical evaluation was accomplished using World Dental Federation (FDI) criteria at baseline and after 6 months, 1, 2, and 3 years. Data were analyzed using Mann–whitney U and Friedman tests (p < 0.05). The success rates were 100% for all resin composite restorations either lined with ion-releasing resin composite or resin-modified glass ionomer liner. Mann–whitney U test revealed that there were no statistically significant differences between both ion-releasing lining material groups for all criteria during the follow-up periods (p > 0.05). Resin composite restorations showed acceptable clinical performance over 3 years either lined with bioactive ionic or resin-modified glass ionomer liners after selective caries excavation preserving pulp vitality. After the 3-year follow-up period, Activa Bioactive and Riva Light Cure liners were clinically effective and they exhibited with the overlying composite restorations successful clinical performance.Trial registration number: NCT05470959. Date of registration: 22/7/2022. Retrospectively registered.