This study researched the effects of Lactobacillus plantarum PMO 08 alone and combined with chia seeds on metabolic syndrome and parameters related to microbiota modulation and intestinal barrier integrity in obese mice fed high-fat diets (HFDs; 45% kcal fat). Male C57BL/6J mice were acclimated for a period of 2 weeks and then randomly separated into five groups depending on whether they received a normal diet (ND group), an HFD (HFD group), an HFD with L. plantarum (PMO group), an HFD with L. plantarum combined with chia seeds (PMOChia group), or an HFD with chia seeds (Chia group). Serum lipid profiles and related markers (cholesterol metabolism-related gene expression) were measured. Intestinal barrier integrity was assessed by measuring occludin mRNA expression of tight junction proteins. Mucosal bacteria were checked with quantitative reverse transcript polymerase chain reaction (qRT-PCR). After 16 weeks of feeding, the PMO group showed significantly lower serum total cholesterol, low-density lipoprotein cholesterol levels, atherogenic index, and cardiac risk factors compared to the HFD group. Moreover, the hepatic mRNA expression of SREBP2 (sterol regulatory element binding protein 2), a protein related to cholesterol metabolism, was significantly downregulated in the PMO group. We also found a positive synergistic effect in the PMOChia group, as manifested by the hepatic mRNA expression of hepatic CYP7A1 (cholesterol 7α-hydroxylase), strengthening of the gut barrier function, and the promotion of more L. plantarum in the colonic mucosa than in either the HFD or PMO group. In conclusion, our results indicate that PMO 08 may protect against metabolic syndrome by exerting effects on the regulation of lipid metabolism. Although the effects of chia seeds alone remain uncertain based on this experiment, its combination with PMO 08 was demonstrated to improve multiple beneficial effects of PMO 08 in obese mice fed HFD, which is a promising possibility for future research.