Bioceramic endodontic cements, known for their antibacterial properties, calcium ion release, and alkaline pH, may come into contact with various irrigants after furcal perforation repair. This study aimed to evaluate the effect of different irrigating solutions and setting times on the shear bond strength (SBS) of Biodentine® (Septodont, Saint-Maur-des-Fosses Cedex, France) to a self-adhering flowable composite. Sixty Biodentine® (Septodont, Saint-Maur-des-Fosses Cedex, France) blocks were prepared and divided into two groups based on the setting time: 72 h and 7 days. These were further subdivided into five subgroups based on the irrigation solution applied: distilled water, sodium hypochlorite, ethylenediaminetetraacetic acid, chlorhexidine, and phosphoric acid. They were then restored with Dyad FlowTM (KerrTM, Orange, CA, USA). SBS and failure modes were assessed at 24 h and 6 months. A two-way analysis of variance (ANOVA) test was performed to analyze the effect of the different irrigating solutions and setting times on the SBS of Biodentine® (Septodont, Saint-Maur-des-Fosses Cedex, France) and Dyad FlowTM (KerrTM, Orange, CA, USA). The level of significance was set at a ≤0.05. At 24 h, SBS was significantly influenced by both the irrigant solution (p = 0.029) and setting time (p = 0.018); at 6 months, SBS was influenced only by the irrigating solutions (p < 0.001). The predominant mode of bond failure was adhesive across all groups. In conclusion, while the setting time did not affect the bond strength, certain irrigating solutions reduced it. Thus, careful consideration of surface treatments applied to Biodentine® is crucial for successful endodontic and restorative outcomes.