The objective of this review is to systematically examine several papers that observe the complex relationships between pharmaceutical treatments and human microbiota, highlighting how these relations may affect the course of treatment. To assure a thorough analysis of the data of current literature, the review was voted for to make use of several databases. PubMed, Open University, Academia Sinica, Southern Methodist University, Yale University, and Google Scholar were the central databases. This study analyzes the 1300 articles from the first search. After eradicating duplicate papers (348), 952 articles endured for abstract screening. After abstracts were observed, 212 publications were excluded. After a full-text screening process, 641 of the 740 remaining articles were estimated ineligible conferring to predetermined inclusion criteria. 99 papers that fulfilled all inclusion requirements were incorporated into the final analysis. The examination of 99 publications published between 2010 and 2023 has provided important new information about the complex interplay among human microbiota and pharmaceutical treatments effectiveness. Even with the countless advancements in microbiome research, there are still numerous unanswered questions. The systematic analysis of 99 publications covering a wide range of medical specialties has significant implications for practical applications as well as guidelines for future study. To understand the dynamic nature of these interactions, longitudinal studies monitoring variations in the composition of the microbiota and medication responses over time are important.