Abstract Purpose To evaluate the association between Gram‐negative enteric rods and Pseudomonas with mucositis and peri‐implantitis, in implants restored with cemented and screw‐retained reconstructions. Materials and Methods Individuals treated with implants, diagnosed with peri‐implant mucositis and or peri‐implantitis, participated in this study. Microbiota from the implant and the gingival sulcus of two neighboring teeth were also studied. The microorganisms were identified using matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry. Results A total of 52 and 51 implants cemented and screwed restored were evaluated in 31 patients. The presence of Gram‐negative enteric rods/Pseudomonas ( P = .01) was significantly higher in the cemented restored implants. When the unit of analysis was the implant, the presence of Gram‐negative enteric rods/Pseudomonas was associated with cemented restored implants after adjustment for possible confounders (odds ratio [OR] = 3.7; 95% CI, 1.4‐10; P = .01); besides, peri‐implantitis was statistically significant in the multivariate model ( P = .008). Considering the patient as a unit of analysis, peri‐implantitis was associated with cemented restored implants (OR = 9.4; 95% CI, 2‐46; P = .006); this statistically significant association remained after adjusting for potential confounders (OR = 6.8; 95% CI, 1.3‐37; P = .02). Conclusion The presence of Gram‐negative enteric rods/Pseudomonas was associated with cemented restored implants; besides, peri‐implantitis was associated with cemented restored implants.