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Cooked common beans (<i>Phaseolus vulgaris</i>) improve intestinal health in lean mice and attenuate intestinal dysbiosis and inflammation when consumed concurrent with obesity development. We determined the effects of a high-fat (HF) bean supplemented diet in mice with established obesity (induced by 12 weeks of HF diet (60% fat as kcal)) compared to obese mice consuming a HF or low-fat (LF) weight loss control diet. Obese C57BL/6 male mice remained consuming HF for eight weeks or were randomly switched from HF to an isocaloric HF with 15.7% cooked navy bean powder diet (HF→HFB) or LF (11% fat as kcal; HF→LF) (<i>n</i> = 12/group). HF→HFB improved the obese phenotype, including (i) fecal microbiome (increased <i>Prevotella</i>, <i>Akkermansia muciniphila</i>, and short-chain fatty acid levels), (ii) intestinal health (increased <i>ZO-1</i>, <i>claudin-2</i>, <i>Muc2</i>, <i>Relmβ</i>, and <i>Reg3γ</i> expression), and (iii) reduced adipose tissue (AT) inflammatory proteins (NFκBp65, STAT3, IL-6, MCP-1, and MIP-1α), versus HF (<i>p</i> < 0.05). Conversely, HF→LF reduced body weight and circulating hormones (leptin, resistin, and PAI-1) versus HF and HF→HFB (<i>p</i> < 0.05); however, AT inflammation and intestinal health markers were not improved to the same degree as HF→HFB (<i>p</i> < 0.05). Despite remaining on a HF obesogenic diet, introducing beans in established obesity improved the obese phenotype (intestinal health and adipose inflammation) more substantially than weight loss alone.