<p>Idiopathic male infertility remains a major challenge in reproductive medicine despite extensive diagnostic workups, prompting research into novel etiologies and interventions. Emerging evidence highlights the microbiome’s role in modulating male reproductive health. This study analyzes global research trends on idiopathic male infertility and associated microbial health over the past two decades using a structured bibliometric approach. Data extracted from Scopus were examined through Biblioshiny and VOSviewer. The analysis reveals a clear transition from traditional genetic and oxidative stress–based studies to microbiome-centered and multi-omics investigations. Increased Research output and citation rates in recent years, underscoring the growing relevance of microbiome studies. Key contributors like Agarwal A, Wang X, Zhang H, and Lundy SD advanced understanding from genetic and oxidative causes to gut-testis and semen microbiome interactions. Leading contributors and countries, particularly China and the USA dominate collaborative networks. Key themes link microbial dysbiosis, oxidative stress, inflammation, and hormonal imbalance with impaired spermatogenesis. Environmental and lifestyle factors, including diet, alcohol, antibiotics, endocrine disruptors, and microplastics, were increasingly recognized as influencing microbiome-mediated fertility. Mechanistic insights into the gut–testis axis, endotoxemia, immune modulation, and nutrient metabolism suggest avenues for diagnostics and microbiome-based interventions, including probiotics, nutritional modulation, and fecal microbiota transplantation.</p> Graphical abstract <p></p>