Germination is a promising strategy to enhance bioactive compound content, particularly γ-aminobutyric acid (GABA) in red rice. However, conventional soaking germination methods are associated with high water consumption and microbial proliferation. This study evaluated the use of a partially circulated germinator with integrated microfiltration and ultraviolet (UV) treatment to process red rice for GABA accumulation while monitoring microbial dynamics. Red rice was germinated for 24, 48, and 72 h under UV and non-UV conditions, with water circulation applied at 90 min intervals for 5 min, and subsequently evaluated for pH, germination performance parameters, GABA content, and microbial quality. Microbial community diversity was characterized in one selected sample using next-generation sequencing (NGS). The results showed that the germinator effectively maintained water pH, mitigated drastic acidification commonly observed in static soaking systems. GABA content increased significantly with germination time, reaching maximum values at 48 h in both systems. Moreover, UV treatment resulted in higher GABA levels at 24 h. Total plate counts in circulation water exceeded 4 log CFU/mL, while reached 9.44 log CFU/g in dried germinated rice. UV treatment of the circulating water successfully reduced microbial load at 24 h germination time. Metagenomic profiling of freshly germinated red rice under non-UV treatment at 48 h revealed dominance of Phytobacter and Enterobacter, linked to seedling growth promotion, followed by Cronobacter spp., which presence suggested potential safety considerations. The findings demonstrate that partial circulation effectively enhances the functional value of red rice with reduced water consumption, offering a more environmentally sustainable alternative to conventional soaking methods.