The aim of this study was to evaluate the effects of three different chemotherapeutic agents, following air‐abrasive debridement, on surface chemical properties and cytocompatibility. Disks contaminated with Streptococcus gordonii biofilm were treated with air‐abrasion and immersion in either 0.9% NaCl (Air + NaCl), 0.05% alkaline electrolyzed water (AEW) (Air + AEW), or 3% H2O2 (Air + H2O2). Noncontaminated and untreated titanium disks served as a control (As‐polished). The efficacy of biofilm removal, magnitude of initial cytocompatibility toward human bone marrow mesenchymal stem cells, and surface chemical properties were determined. In all treatment groups, biofilms containing microorganisms were observed to be completely removed. The data showed discrepancies for cell affinities among treatment groups, whereby: (1) the number of cells attached to the Air + AEW treated surfaces was approximately two times greater than that to the Air + NaCl treated surfaces; and (2) cell spreading was significantly enhanced on the Air + AEW treated surfaces compared with the Air + NaCl or Air + H2O2 treated surfaces. X‐ray photoelectron spectroscopy data showed that the mean relative concentrations of nitrogen to titanium on the As‐polished, Air + NaCl, Air + AEW, and Air + H2O2 surfaces were 0.0079, 0.0237, 0.0071, and 0.0210, respectively, which would provide a clear understanding that these discrepancies could be attributed to sufficient removals of organic‐nitrogen deposits at the same magnitude as the As‐polished following the Air + AEW treatment. This study clarifies that chemical surface treatment with AEW, as an adjunctive to air‐abrasive debridement may be beneficial in restoring surface properties for tissue integration. © 2019 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 108B:183–191, 2020.