Display omitted Preventive effects of co-administration of GTE with IMOs against HFD-induced alterations in mice. Administration of GTE with IMOs to HFD-fed mice prevented diet induced pathologies across multiple organ system. Its supplementation prevented adipose tissue mass building and prevented systemic obesity. It also prevented HFD-induced alteration in insulin, glucagon and leptin levels. In liver, GTE with IMOs most effectively prevented HFD-induced lipid and glucose metabolism aberrations, inflammation (via NF-kB pathway activation) and metabolites patterns. Systemically, it prevented HFD-induced increase in pro-inflammatory cytokines and reduction in anti-inflammatory adipokines. Its supplementation also prevented HFD-induced impairment in glucose tolerance and in turn improved insulin sensitivity. It also prevented HFD-induced gut microbial dysbiosis along with structural damages and SCFAs production. A reduced lipopolysaccharide production further assisted towards improved insulin sensitivity and reduced systemic inflammation. High fat diet (HFD)-induced alterations in gut microbiota and resultant ‘leaky gut’ phenomenon promotes metabolic endotoxemia, ectopic fat deposition, and low-grade systemic inflammation. Here we evaluated the effects of a combination of green tea extract (GTE) with isomalto-oligosaccharide (IMOs) on HFD-induced alterations in mice. Male Swiss albino mice were fed with HFD (58% fat kcal) for 12 weeks. Systemic adiposity, gut derangement parameters and V3-V4 region based 16S rRNA metagenomic sequencing, ectopic fat deposition, liver metabolome analysis, systemic and tissue inflammation, and energy homeostasis markers along with gene expression analysis in multiple tissues were done in mice supplemented with GTE, IMOs or their combination. The combination of GTE and IMOs effectively prevented HFD-induced adiposity and lipid accumulation in liver and muscle while normalizing fasting blood glucose, insulin, glucagon, and leptin levels. Co-administration of GTE with IMOs effectively modulated liver metabolome associated with lipid metabolism. It also prevented leaky gut phenotype and HFD-induced increase in circulating lipopolysaccharides and pro-inflammatory cytokines (e.g. resistin, TNF-α, and IL-1β) and reduction in anti-inflammatory cytokines (e.g. adiponectin and IL-6). Gene expression analysis across multiple tissues further supported these functional outcomes. Most importantly, this combination improved beneficial gut microbiota (Lactobacillus sp., Bifidobacteria, Akkermansia muciniphila, Roseburia spp.) abundances, restored Firmicutes/Bacteriodetes and improved Prevotella/Bacteroides proportions. In particular, a combination of these two agents has shown improved beneficial effects on multiple parameters studied. Data presented herein suggests that strategically chosen food components might be highly effective in the prevention of HFD-induced alterations and may further be developed as functional foods.