To modify an adhesive system with halloysite clay nanotubes (HNTs) containing arginine and calcium carbonate and to evaluate their cytocompatibility, viscosity and efficacy in reducing dentin permeability. HNTs containing arginine and calcium carbonate were incorporated into the primer and adhesive of a three‐step adhesive system (SBMP), and their viscosity was measured. Discs (n = 4/group) were prepared: SBMP (control), HNT‐PR (modified primer), HNT‐ADH (modified adhesive) and HNT‐PR + ADH (modified primer and adhesive) were evaluated regarding cell death and viability. Dentin discs were prepared and randomly assigned into the following treatments (n = 10): NC (no treatment), SBMP, HNT‐PR, HNT‐ADH, HNT‐PR + ADH and COL (Colgate® Sensitive Pro‐relief™ prophylaxis paste). After, they were submitted to an erosive‐abrasive cycling. Dentin permeability (hydraulic conductance) was evaluated at baseline, 24 h after treatment and after cycling. Both the modified primer and adhesive showed significantly higher viscosity than their controls. Group HNT‐PR resulted in significantly higher cytotoxicity when compared to SBMP and HNT‐PR + ADH groups. Group HNT‐ADH resulted in the highest cell viability compared to all other groups. All groups showed significantly lower dentin permeability when compared to the NC group. Post‐cycling, SBMP and HNT‐ADH groups showed significantly lower permeability when compared to COL group. The addition of encapsulated arginine and calcium carbonate did not affect the cytocompatibility of the materials nor their ability to reduce dentin permeability.