Western-style diets are associated with metabolic syndrome, characterized by obesity and hyperglycemia, which is a major public health problem in the 21st century. Recent studies have proven that probiotics have promising effects in the management of metabolic syndrome. This study aimed to investigate the effects of Bacillus coagulans BC69 on the metabolic and histological alterations associated with metabolic syndrome in C57BL/6J mice fed with a high-sugar and high-fat (HSHF) diet. The body weight, biochemistry, histology, and gut microbiome were assessed. The results showed that administration of BC69 from the first week reduced body weight gain, liver weight, and production of pro-inflammatory cytokines (TNF-α), and restored faecal acetate and butyrate concentrations in mice. Histological sections showed that BC-69 also reduced HSHF-induced liver pathological damage in mice by improving hepatocyte disorganization and reducing inflammatory cell infiltration. In addition, 16S rRNA gene sequencing showed that BC69 improved the gut microbiome of HSHF diet-fed mice. This study revealed that BC69 has the potential to be a safe and effective tool in the treatment of metabolic syndrome.