Aging is associated with alterations in gut microbiota, yet the combined effects of geography and diet remain underexplored in elderly populations. This study investigated the gut microbiota of 227 healthy Vietnamese individuals aged ≥60 years, stratified by select urban and rural residence in both Hanoi and Thanh Hoa provinces, and across three age groups (60–69, 70–79, ≥80 years). Dietary patterns were collected and recorded for each participant. 16S rRNA gene sequencing revealed significant differences in microbial diversity and composition associated with geographical location (urban, rural) and age. Urban participants in Hanoi exhibited higher richness and greater abundance of health-associated genera, including Bifidobacterium, Fusicatenibacter, and Blautia, likely reflecting more diverse plant-based diets. In contrast, rural participants in Thanh Hoa showed enrichment of beneficial butyrate-producing genera such as Fusicatenibacter, Roseburia, Lachnospira and Blautia, possibly linked to traditional diets rich in freshwater fish and fermented foods. Participants aged 70–79 years displayed reduced microbial richness compared to other age groups. Age-related reductions in Roseburia, Veillonella, and Prevotella were also observed. These findings highlight how geography, diet, and aging shape the gut microbiota and may guide microbiota-targeted dietary strategies to promote healthy aging.