This systematic review assesses the microbiological similarities and differences between healthy and diseased peri-implant sulci based on available literature evidence. A thorough electronic search was conducted in databases such as PubMed, Google Scholar, and Cochrane; a manual search employing eligibility criteria was conducted as well. After a comprehensive review, studies evaluating the microbial profile obtained from biofilm samples from healthy and diseased peri-implant sulci were chosen. Ten articles compared microbial profiles of healthy and failing implants. A statistically significant variation in the microbial profile was observed, with predominating Gram-negative, anaerobic organisms at both the genus and species level between healthy and diseased peri-implant sulci. Also, red complex organisms (<i>P. gingivalis, T. forsythia,</i> and <i>P. intermedia</i>) predominated in diseased peri-implant sulci. According to existing studies, peri-implantitis is characterized by a diverse microbial community that includes obligate anaerobic Gram-negative bacteria such as <i>T. denticola, T. forsythia, P. gingivalis,</i> and <i>P. intermedia</i>. This research will pave the way for further studies assessing specific bacterial flora in diseased peri-implant sulci, which will help in developing specific treatment targets for peri-implantitis.