This study evaluated the effect of dentin surface treatment on the micromorphology and shear bond strength (SBS) of a self-adhering flowable composite, Vertis Flow (VF). Flat dentin surfaces obtained from sixty extracted human molars were divided into six groups (n = 10) according to the following surface treatments: (G1) control, no treatment; (G2) self-etching adhesive, Optibond All-in-One; (G3) phosphoric acid etching for 15 s; (G4) polyacrylic acid for 10 s; (G5) EDTA for 60 s; and G6) sodium hypochlorite (NaOCl) for 15 s. After restoration using VF, SBS was measured in MPa. Data were analyzed using one-way ANOVA and Tamhane test (α = 0.05). Six additional specimens were prepared for scanning electron microscopy analysis. SBS was significantly affected by surface treatment (P < 0.001). SBS of six groups from the highest to the lowest were as follows: (G3) 13.5(A); (G5) 8.98(AB); (G2) 8.85(AB); (G4) 8.21(AB); (G1) 7.53(BC); and (G6) 4.49(C) (groups with the same superscript letter were statistically similar). Morphological analysis revealed numerous long resin tags at the adhesive interface for acid-etched group, with a few short resin tags for the control group and small gap formation for NaOCl-treated group. In conclusion, dentin surface treatments tested differently affected bonding performance of VF; only acid-etching effectively improved this.