This study aimed to compare the efficacy of fermented cow milk and fermented soy milk as protective carriers for the probiotic strain, Lactiplantibacillus plantarum LP-6 (LP-6), during upper gastrointestinal digestion. Using a near-real dynamic in vitro human stomach system, we evaluated the survival of LP-6 in fermented soy milk and fermented cow milk under simulated upper gastrointestinal conditions. Additionally, we conducted metabolomics analysis at different digestion stages to investigate the potential mechanisms of probiotic survival. Our results revealed that soy milk outperformed cow milk as a carrier, significantly improving the survival of LP-6 throughout digestion. The metabolomics analysis revealed notable enrichment in aspartic acid, glutamate, glutamine, phenylalanine metabolism, and ABC transporter proteins in digested fermented soy milk compared to digested fermented cow milk. These changes likely contribute to enhanced acid tolerance and bacterial cell protection in fermented soy milk. Our findings suggest that soy milk is an optimal carrier for LP-6, effectively protecting specific strains from acid stress while ensuring efficient delivery.