ObjectivesTo assess the association between Gram‐negative enteric rods and Pseudomonas with the clinical parameters in peri‐implant disease.Materials and MethodsPatients treated with implants and diagnosed with peri‐implant mucositis and/or peri‐implantitis participate in this cross‐sectional research. Unusual microorganisms from the implants were recognized using MALDI‐TOF mass spectrometry. Linear regression models were applied.ResultsA total of 103 implants were evaluated in thirty‐one participants. Gram‐negative enteric rods/Pseudomonas were observed in 47 implants (46%). Interestingly, there were differences in probing pocket depth (PPD), clinical attachment loss (CA), and bleeding on probing (BOP) between the groups, where implants with the presence of Gram‐negative enteric rods/Pseudomonas presented deteriorated clinical parameters (p < .0001). The crude and adjusted linear regression models for PPD in peri‐implant mucositis, PPD in peri‐implantitis, CA in peri‐implantitis, and BOP in peri‐implant disease present significant βs, demonstrating deteriorated parameters (p < .0001) in the presence of Gram‐negative enteric rods/Pseudomonas. Besides, the model for CA in peri‐implantitis showed that cemented restored reconstructions were statistically significant (p = .009). Additionally, the R2 value in most models indicated a high degree of correlation (>85%).ConclusionThe occurrence of Gram‐negative enteric rods and Pseudomonas was associated with deteriorated clinical parameters in patients with peri‐implant disease.