Kefir is a functional fermented dairy product whose health-promoting properties can be enhanced through fortification with plant-derived bioactive compounds. Etlingera elatior (torch ginger) represents a promising botanical source due to its rich phytochemical content. This study aimed to evaluate the effects of torch ginger tea (TGT) supplementation on the physicochemical, microbial, and metabolic characteristics of kefir. A comparative analysis between control kefir (CK) and TGT-supplemented kefir was conducted using an integrated approach, including physicochemical and sensory evaluations, as well as metagenomic and untargeted LC-MS metabolomic analyses. The results showed that TGT significantly increased moisture and ash content while reducing total soluble solids and color intensity. The microbial community remained stable, with no significant differences observed in alpha and beta diversity. However, TGT selectively modulated the microbiota by increasing the abundance of beneficial lactic acid bacteria and suppressing non-lactic acid bacteria. Metabolomic analysis further revealed a clear separation between treatments and identified key differential metabolites, including fatty acids and caffeine as a plant-derived marker. These findings highlight plant–microbe interactions as a key mechanism influencing fermentation dynamics and metabolic outcomes, supporting the potential of TGT as a functional ingredient for the development of innovative kefir-based products.