Background Lasers represent a promising method for implant decontamination, but evidence on implant surface changes and subsequent biofilm formation is limited. This study aimed to assess the effect of erbium‐doped yttrium aluminum garnet (Er:YAG) laser treatment on zirconia and titanium discs, and the differences in biofilm formation as a result of surface alterations. Methods A two‐stage (in vitro and in vivo) experiment utilizing Er:YAG laser on titanium and zirconia discs was performed. In vitro, surface alterations, roughness, and elemental‐material weight differences following laser treatment were assessed using scanning electron microscopy and atomic force microscopy. In vivo, four participants wore custom‐made intra‐oral stents, embedded with laser‐treated and untreated titanium and zirconia discs overnight. Biofilm‐coated discs were stained using nucleic acid fluorescence dye and visualized using multiphoton confocal laser scanning microscopy. Biofilm 3D structure, biomass, thickness, and live‐to‐dead bacteria ratio were assessed. Results Both titanium and zirconia discs treated with Er:YAG laser resulted in visual surface alterations, but showed no significant change in average surface roughness (titanium P = 0.53, zirconia P = 0.34) or elemental‐material‐weight (titanium, P = 0.98), (zirconia, P = 0.96). No significant differences in biofilm biomass, average thickness, and live‐to‐dead bacteria ratio of laser‐treated titanium and zirconia discs were identified compared to untreated groups (titanium P > 0.05, zirconia P > 0.05). Generally, zirconia discs presented with a lower live‐to‐dead bacteria ratio compared to titanium discs, regardless of laser treatment. Conclusion Er:YAG laser treatment of titanium and zirconia implant surfaces does not significantly affect surface roughness, elemental material weight, or early biofilm formation in the oral cavity.

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