Yogurt offers potential health benefits, particularly for the intestines. The choice of starter culture is key to the production of functional yogurt. In this study, Lactiplantibacillus plantarum ZFM55 was incorporated into a commercial starter and its effects on the quality of yogurt was evaluated. Changes in texture, flavor, composition, and metabolites were assessed, along with its impact on the gut microbiota. We found adding ZFM55 improved the water holding capacity, cohesiveness, viscosity, and hardness of the yogurt. Analysis using gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) and liquid chromatography-mass spectrometry (LC-MS) demonstrated that ZFM55 contributed to a desirable flavor profile and increased the levels of non-volatile metabolites, such as amino acids and carbohydrates. Stool samples from volunteers who consumed fermented milk were collected and analyzed using 16 S rDNA sequencing and GC-MS. The results showed that fermenting yogurt with ZFM55 significantly altered the beta diversity of the gut microbiota. Notably, probiotics such as Bifidobacterium, Blautia, and Lactobacillus exhibited substantial increases, along with a notable rise in the production of short-chain fatty acids, particularly acetic acid and butyric acid. These findings highlight the potential of ZFM55 for developing high-quality functional yogurt products.