This review provides a comprehensive analysis of the microbiota associated with healthy peri-implant tissues, peri-implant mucositis, and peri-implantitis. Healthy peri-implant sites are predominantly colonized by Gram-positive cocci and facultatively anaerobic rods, forming a stable community that prevents pathogenic colonization. Peri-implant mucositis is characterized by increased microbial diversity, including both health-associated and pathogenic bacteria, leading to early tissue inflammation. Peri-implantitis is marked by even greater microbial diversity and a complex pathogenic biofilm, with predominant pathogens including Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, and Fusobacterium nucleatum. Other species such as Staphylococcus and Enterobacteriaceae contribute to disease progression through biofilm formation and increased inflammatory response. Additionally, Candida albicans, Herpes Simplex Virus (HSV), and Epstein–Barr Virus (EBV) play roles in peri-implantitis through biofilm formation, immune modulation, and synergistic interactions. The review emphasizes the importance of standardizing diagnostic criteria, employing advanced molecular techniques, integrating microbial data with clinical factors, and understanding inter-kingdom interactions for effective prevention and treatment strategies. Microbiological sampling and analysis techniques, including culture-based methods and next-generation sequencing, have provided insights into the complex microbial communities involved in peri-implant diseases. The microbial profiles of healthy peri-implant sites, peri-implant mucositis, and peri-implantitis differ significantly, with healthy sites showing a more stable and less pathogenic microbiota. The review highlights the need for comprehensive antimicrobial strategies that address both bacterial and fungal components of the infection, as well as the role of viral pathogens in peri-implantitis. Understanding these microbial profiles is crucial for developing effective therapeutic approaches to maintain peri-implant health and prevent disease progression.This review provides a comprehensive analysis of the microbiota associated with healthy peri-implant tissues, peri-implant mucositis, and peri-implantitis. Healthy peri-implant sites are predominantly colonized by Gram-positive cocci and facultatively anaerobic rods, forming a stable community that prevents pathogenic colonization. Peri-implant mucositis is characterized by increased microbial diversity, including both health-associated and pathogenic bacteria, leading to early tissue inflammation. Peri-implantitis is marked by even greater microbial diversity and a complex pathogenic biofilm, with predominant pathogens including Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, and Fusobacterium nucleatum. Other species such as Staphylococcus and Enterobacteriaceae contribute to disease progression through biofilm formation and increased inflammatory response. Additionally, Candida albicans, Herpes Simplex Virus (HSV), and Epstein–Barr Virus (EBV) play roles in peri-implantitis through biofilm formation, immune modulation, and synergistic interactions. The review emphasizes the importance of standardizing diagnostic criteria, employing advanced molecular techniques, integrating microbial data with clinical factors, and understanding inter-kingdom interactions for effective prevention and treatment strategies. Microbiological sampling and analysis techniques, including culture-based methods and next-generation sequencing, have provided insights into the complex microbial communities involved in peri-implant diseases. The microbial profiles of healthy peri-implant sites, peri-implant mucositis, and peri-implantitis differ significantly, with healthy sites showing a more stable and less pathogenic microbiota. The review highlights the need for comprehensive antimicrobial strategies that address both bacterial and fungal components of the infection, as well as the role of viral pathogens in peri-implantitis. Understanding these microbial profiles is crucial for developing effective therapeutic approaches to maintain peri-implant health and prevent disease progression.