Background: The deep margin elevation (DME) technique provides advantages for root canal treatment, but the impact of applied irrigation protocols on bonding for subsequent restorations is a significant concern. The aim of this in vitro study was to test the bond strength of a flowable resin material used in DME restorations after composite restorations were exposed to different irrigation protocols. Methods: Standard composite samples (G-aenial® Universal Injectable) were divided into nine groups according to irrigation protocols. Untreated composite sample were used as control. The group A were kept in 5.25% sodium hypochlorite (NaOCl) and the group B were kept in 3.5% chlorine dioxide (ClO2) for 30 min. Then, the following treatment protocols were applied to the subgroups, respectively. Group1A/B: 17%EDTA + 5.25%NaOCl + Distilled Water + 2%CHX, Group2A/B: 18%HEDP + 5.25%NaOCl + Distilled Water + 2%CHX, Group3A/B: 17%EDTA + 3.5%ClO2 + Distilled Water + 2%CHX, Group4A/B: 18%HEDP + 3.5%ClO2 + Distilled Water + 2%CHX. After irrigation procedures, samples were washed with distilled water and sandblasted. G-Premio Bond and composite restorations (G–aenial® A’CHORD) were applied. The samples were then cut perpendicular to the interface with an IsoMet® low speed diamond saw under water. For the microtensile bond strength test, rectangular sticks with an average cross-sectional area of ∼1 mm2 will be obtained. The first section with 1-mm thickness was excluded to prevent its possible confounding effect on the results. Three sections were obtained of each sample (n = 15) and tested for microtensile bond strength. The analysis of the data collected in accordance with the purpose of the study was performed with One-way ANOVA (n = 15). For multiple comparisons between groups, it was evaluated with Tukey HSD test. Results: Groups A1 and A2, immersed in NaOCl for 30 min, showed statistically significantly lower bond strength compared to Group B3, immersed in ClO₂ for 30 min, and the control group (P < 0.05). The use of ClO₂ irrigation is recommended due to its positive effects on bond strength. Conclusion: Prolonged NaOCl irrigation may adversely affect the bond strength of flowable composites used for deep margin elevation.