Desensitizing agents are frequently applied to sensitive teeth and may affect subsequent resin bonding. The current study aimed to evaluate the bonding performance of two self-etch adhesives containing functional monomers to dentine pretreated with three new calcium-containing desensitizers. No desensitizer was applied in the control group. Groups 1, 2, and 3 were treated with an arginine–calcium carbonate-containing polishing paste, a casein phosphopeptide–amorphous calcium phosphate (CPP-ACP)-containing paste, and an experimental hydroxyapatite paste, respectively. G-Bond and Clearfil S3 Bond were used for bonding after desensitizer treatments. The microtensile bond strength (μTBS) was tested (n = 20 beams per group) and failure mode distribution was analyzed. Scanning electron microscopy was used to observe the occlusion of dentinal tubules. The mean (±SD) μTBS values, expressed in MPa, of groups 1, 2, and 3 and the control group were, respectively, 30.81 (7.79), 44.41 (8.02), 31.49 (6.13), and 41.40 (8.67) for G-Bond and 39.63 (9.59), 32.55 (7.86), 37.50 (8.60), 27.90 (6.52) for S3 Bond. Most failures were recorded as adhesive failure (69.375%), instead of cohesive failure or mixed failure. The dentinal tubules were seldom plugged in group 2, but were mostly occluded in groups 1 and 3. Two-way anova indicated that desensitizer application in association with a compatible adhesive system should be used when endeavoring to control hypersensitivity without adverse interference in bonding.