(1) Background: this study aims to test the cytotoxicity of three antimicrobial products used in periodontitis treatment on gingival mesenchymal stem cells (gMSCs) and their influence on root surfaces and gMSC adhesion. We tested the null hypothesis that the effects of the antimicrobials did not differ. (2) Methods: the commercial products based on sulphonic/sulphuric acids, sodium hypochlorite and silver nanoparticles, in five different concentrations, were added to culture medium for growing gMSCs. Cell proliferation capacity was tested using the Cell Counting Kit-8 (CCK8) and their viability was determined by succinate dehydrogenase activity (MTT) assay. Scanning electron microscopy evaluated the adhesion of gMSCs on root samples treated mechanically and with commercial products. (3) Results: the products induced a dose-dependent cytotoxicity in terms of reduced proliferation and viability of gMSCs, as well as cell shape modifications. Significant differences in CCK8 values between the different commercial products were observed. Based on proliferation tests, the null hypothesis was rejected. When MTT values of the three products were compared with each other, no significant differences were observed for any of the five concentrations (p = 0.065, p = 0.067, p = 0.172, p = 0.256, p = 0.060). (4) Conclusions: the three antimicrobials had a certain degree of cytotoxicity on gMSCs. gMSCs repopulated treated root surfaces.