Peri-implant mucositis and peri-implantitis are the main biological complications associated with dental implants. Since most authors agree that bacteria play a major etiological role, the main aims of this study were to determine if a formulation of erythritol and chlorhexidine applied with an air polishing system inhibits biofilm regrowth over dental implants and to compare the decontamination capacity of this therapy with that of mechanical removal by saline and gauze. A multispecies biofilm (P. gingivalis, A. actinomycetemcomitans, F. nucleatum, A. naeslundii, V. parvula and S. oralis) was grown for 14 days on 52 dental implants in an artificial mouth. These implants were divided into three groups according to the applied treatment: 14 negative control (CON), 19 erythritol-chlorhexidine (ERY) and 19 gauze with saline (GAU) samples. Twelve dental implants from the ERY and GAU groups and 8 implants from the CON group were re-incubated for 7 additional days after treatment. The bacterial count was performed by quantitative polymerase chain reaction (qPCR) using propidium monoazide (PMA). A descriptive and bivariate analysis of the data was performed. The erythritol and chlorhexidine formulation significantly inhibited biofilm regrowth in comparison with the mechanical treatment (GAU), since a significant decrease in all the species was observed in the ERY group (except for Aggregatibacter actinomycetemcomitans). The antibiofilm and antibacterial capacity of the two active treatment groups (ERY and GAU) was similar for a 14 days multispecies in vitro biofilm, except for the lower count of A. naeslundii in the GAU group. The use of erythritol powder with chlorhexidine applied with an air polishing system reduces biofilm regrowth over dental implants when compared with mechanical removal by saline and gauze. This effect might be beneficial for patients included in peri-implant maintenance programs.