Abstract Background Current peri‐implantitis treatment methods are modeled after dental cleaning modalities like abrasive surface cleaning. However, mechanical abrasive cleaning not only inadequately removes implant biofilms but also compromises implant surface integrity with adverse biological effects. The goal of this study was to evaluate a non‐abrasive waterjet implant cleaning method to remove biofilm while preserving titanium surface and maintaining its cytocompatibility. Methods Dental plaque‐derived multispecies biofilms were cultured on acid‐etched titanium disks. Biofilm was removed using either mechanical contact abrasive implant cleaning (titanium brush or curette) or a non‐contact waterjet irrigator in continuous or pulsed flow setting. Uncontaminated and untreated disks served as negative and positive controls, respectively. Bacterial viability post‐treatment was assessed by agar plating and live‐dead imaging. Titanium surface integrity was studied by scanning electron microscopy and optical profilometry. Host tissue compatibility was evaluated by human gingival fibroblast proliferation on titanium surface post‐cleaning. Results Non‐contact waterjet irrigation significantly reduced viable bacterial counts by ≥90.9% (∼100‐fold) on titanium surface versus abrasively cleaned and untreated biofilm groups (all p < 0.05). Waterjet treatment maintained titanium surface integrity and roughness similar to pristine titanium. In contrast, abrasive cleaning damaged the microrough titanium surface and left viable bacterial residues. Fibroblast viability was restored (∼76.8%) on waterjet‐treated titanium to levels comparable to sterile control ( p > 0.05), whereas titanium brush‐ or curette‐treated surfaces had significantly lower levels post‐cleaning (all p < 0.05). Conclusions Non‐abrasive waterjet cleaning is a superior method for the clinical treatment of peri‐implantitis biofilms versus mechanical abrasive cleaning while maintaining titanium implant surface properties necessary for reintegration with peri‐implant tissue. Plain Language Summary Dental implant infections are usually cleaned by scrubbing the implant surface to remove attached bacteria. However, this mode of cleaning can scratch the implant surface and produce tiny pieces of wear or particles which can be toxic and cause the implant to fail. In this study, a new cleaning method using a fast‐flowing stream of water, called waterjet cleaning, was tested. The waterjet cleaning was able to remove most bacteria from the implant material, while cleaning by scrubbing left small spots of bacteria on the surface. Additionally, waterjet‐cleaned surfaces looked like the original implant material surface, while scrubbing‐cleaned surfaces had pieces missing from the surface, which affected human gum tissue cells attachment. Waterjet cleaning is a favorable method to clean dental implant infections without damaging the implant and allow for human tissue to recover and reconnect with the dental implant.