Obesity is a pandemic metabolic syndrome with increasing incidences every year. Among the significant factors that lead to obesity, overconsumption of high-fat food in daily intake is always the main contributor. Functional foods have shown a positive effect on disease prevention and provide health benefits, including counteracting obesity problem. Vinegar is one of the fermented functional beverages that have been consumed for many years, and different types of vinegar showed different bioactivities and efficacies. In this study, we investigated the potential effects of pineapple vinegar as an antiobesity agent on a high-fat diet- (HFD-) induced C57BL/6 obese mice. C57BL/6 mice were treated with pineapple vinegar (1 mL/kg BW and 0.08 mL/kg BW) for 12 weeks after 24 weeks of HFD incubation. Serum biochemistry profiles, antioxidant assays, qPCR, proteome profiler, and 16S metagenomic were done posttreatment. Our data showed that a high concentration of pineapple vinegar (1 mL/kg BW) treatment significantly (p < 0.05) reduced the bodyweight (∼20%), restored lipid profiles, increased the antioxidant activities, and reduced the oxidative stress. Besides, significant (p < 0.05) regulation of several adipokines and inflammatory-related genes was recorded. Through the regulation of gut microbiota, we found a higher abundance of Akkermansia muciniphila, a microbiota reported to be associated with obesity in the high concentration of pineapple vinegar treatment. Collectively, these data established the mechanism of pineapple vinegar as antiobesity in mice and revealed the potential of pineapple vinegar as a functional food for obesity.