This study evaluated the effect of 2% chlorhexidine gluconate-based cavity disinfectant (CHX) on the microtensile bond strength (TBS) of glass ionomer, resin-modified glass ionomer and packable resin composite to sound and caries-Affected dentin. Sound and occlusal caries-Affected human third molars (N = 36, n = 3 per group) were randomly divided into three experimental groups to receive one of the following restorative materials. (a) Glass ionomer (Ketac Molar, 3 M ESPE; GI), (b) resin-modified glass ionomer (Vitremer, 3 M ESPE; RMGI) and (c) packable resin composite (Surefil, Dentsply; PRC) with a bonding agent (Prime Bond NT, Dentsply De Trey). Caries was removed using a caries-detecting dye (Caries Detector, Kuraray Medical Ltd.) and flat dentin surfaces were achieved by finishing up to 1200-grit silicon carbide abrasive. Half of the teeth in each group received 2% CHX (Consepsis, Ultradent). Dentin surfaces were built-up with the respective materials incrementally and were sectioned with a slow-speed saw into multiple beams. The beams were subjected to TBS test (0.5 mm/min) in a Universal Testing Machine. The data were analysed using two-way analysis of variance and Tukeys tests. For each restorative material, TBS results were not affected by the application of CHX (p > 0.05) on both sound and caries-Affected dentin (p > 0.05). PRC in combination with the corresponding bonding agent showed significantly higher results (p < 0.05) than those of GI and RMGI, on sound and caries-Affected teeth, respectively. Cohesive failure in dentin was not observed in any of the groups. The use of 2% chlorhexidine-based cavity disinfectant did not impair the adhesion of the restorative materials tested to either sound or caries-Affected dentin.