The human gut microbiota, a diverse ecosystem of microorganisms, has become a focal point in pharmacological research due to its influence on drug metabolism and therapeutic efficacy. This systematic review synthesizes findings from 150 clinical and preclinical studies to understand how alterations in gut microbiota impact drug metabolism and clinical outcomes. A meta-analysis revealed significant microbiota-dependent variability in drug metabolism, with a pooled standardized mean difference (SMD) of 0.45 (95% CI: 0.30–0.60, p < 0.001). Chemotherapeutic agents, such as irinotecan, exhibited the most significant effects, with microbial enzymes, like β-glucuronidases, playing a critical role in the reactivation of toxic drug metabolites. Additionally, gut microbiota influences the bioavailability of other drugs, such as digoxin, which is inactivated by Eggerthella lenta. The review also highlights the potential of microbiota-modulating interventions, such as probiotics and fecal microbiota transplantation (FMT), to optimize therapeutic outcomes. These findings emphasize the need for microbiota profiling in personalized medicine and the development of standardized microbiota-modulating therapies for better drug efficacy and reduced toxicity.