Background: Gut microbiota plays a critical role in host metabolism, immunity, and intestinal barrier integrity. Both chronic kidney disease (CKD) and kidney transplantation (KTR) are associated with gut dysbiosis, driven by uremic toxins, comorbidities, and immunosuppressive therapy. However, direct comparisons between hemodialysis (HD), KTR, and healthy controls (HC), while accounting for dietary factors, remain limited. Methods: We conducted a cross-sectional study including 48 HD patients, 75 KTR patients, and 13 HC. Stool patient samples were analyzed using 16S rRNA amplicon sequencing targeting the V4-V4 region to assess microbial composition and diversity. Data on clinical status, laboratory parameters, and dietary intake were collected and integrated with microbiome profiling. Results: Firmicutes and Bacteroidota dominated all groups, with Akkermansia enriched in HD and SCFA-producing genera (Faecalibacterium, Roseburia) more abundant in KTR. LEfSe and sPLS-DA analyses identified Akkermansia and Clostridia-related taxa as discriminants of HD, while Acidaminococcus and Megasphaera characterized KTR. HD patients exhibited higher alpha diversity (Faith’s PD and Chao1) than KTR (p < 0.05). Dietary intake differed across groups, but explained only a small proportion of microbial variance. Conclusions: Both HD and KTR patients display persistent gut dysbiosis with distinct microbial signatures. While transplantation partially restores SCFA producers, immunosuppression and diet shape new ecological shifts. These findings underscore the potential of microbiota as a biomarker and therapeutic target in renal replacement therapies.