PurposeTo evaluate the effect of adding nano-chitosan on different properties of the adhesive and high-filled flowable composite resin (viewing the graphical abstract is suggested). BackgroundIncorporating chitosan might improve the quality of adhesive and high-filled composite resin used in the deep margin elevation (DME) and other restorative methods. Materials and methodsTwo groups of composite disks (without chitosan, with 1 % chitosan) were created to evaluate antimicrobial effects, degree of conversion (DC), solubility and water sorption. Antimicrobial activity was evaluated through biofilm inhibition and disk agar diffusion tests while DC was analyzed using FTIR. For the microshear bond strength test (μSBS), extracted maxillary molars were sectioned 1 mm under the CEJ, undergoing immediate dentin sealing and DME in four groups: control, pretreatment chitosan application, adhesive+1 % chitosan, and composite+1 % chitosan. The forces and the modes of failure were recorded. ResultsAdding chitosan nanoparticles increased the antimicrobial activity, significantly (p < 0.05). The μSBS and DC did not differ significantly between the groups (p > 0.05), and the failures were mostly found in the adhesive mode. The solubility and water sorption increased significantly (p < 0.05), remaining in a clinically acceptable range though. ConclusionAdding chitosan could be a potential option to increase the antibacterial effect in the high-filled composite resin without any negative affect on μSBS or DC, and clinically unacceptable effect on solubility and water sorption. (The graphical abstract has been provided). Clinical significanceAdding chitosan nanoparticles to high-filled flowable composite resin, increases the success rate of related restorative technique by adding the antimicrobial effect without any significant negative influence on other biomechanical properties.