To assess longitudinal peri-implant tissue evaluation in a plaque compromised ligature free dog model, clinically, radiographically, microbiologically and histologically. Six beagle mandibular premolars and first molars were extracted. Plaque accumulated for 16 weeks. Two implants were placed per hemi-mandible. For 17 weeks, control implants (CI) in one hemi-mandible were brushed daily; test implants (TI) in the other were not. These parameters were then assessed: clinically, probing depth (PD), bleeding-on-probing (BOP), presence of plaque (PP) and clinical attachment level (CAL); radiographically, marginal bone level; microbiologically, counts for Streptococcus spp., Fusobacterium spp., Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, Prevotella intermedia and total bacterial load. At week 17, histomorphometric analysis was performed (MM-ISH (mucosal margin-implant shoulder); ISH-fBIC (implant shoulder-first bone-to-implant contact); MM-aJE (mucosal margin-apical area junctional epithelium); MM-aINF (mucosal margin-apical limit of the inflammatory infiltrate); %INF (percentage of inflammatory infiltrate)). At week 17, TI had significant increased PD, BOP, PP and CAL versus baseline. All clinical variables presented intergroup differences. There was no intergroup difference for radiographic bone loss (p > 0.05). Total bacteria, Fusobacterium spp., A. actinomycetemcomitans and P. gingivalis had intergroup differences. There was no statistically significant intergroup difference for ISH-fBIC. Longitudinal microbiology evaluation detected a shift period. Final intergroup microbiological differences were the basis of W17 clinical intergroup differences, with higher values in TI. Microbiological and clinical changes detected in peri-implant tissues were compatible with onset of peri-implant disease. Despite histological inflammatory intergroup difference, no histological or radiographic intergroup bone loss was detected. This study set-up describes a valuable method for generating "true" early peri-implant defects without mechanical trauma.