Background Milk fat globule membrane (MFGM) is a phospholipid-rich component of dairy fat that may explain the benefits of full-fat dairy products on cardiometabolic risk. Preclinical studies support MFGM to decrease gut permeability, which may attenuate gut-derived endotoxin translocation and consequent inflammatory responses that impair cardiometabolic health. Objective To describe the rationale, study design, and planned outcomes that will evaluate the efficacy of MFGM-enriched milk versus a comparator beverage on health-promoting gut barrier functions in persons with metabolic syndrome (MetS). Methods We plan a double-blind, randomized cross-over trial (ClinicalTrials.gov: NCT03860584) in which MetS persons will receive a rigorously controlled eucaloric diet for 2-wk that contains 3 daily servings of an MFGM-enriched bovine milk beverage or a comparator beverage that is formulated with non-fat dairy powder, coconut and palm oils, and soy phospholipids. Compliance will be monitored by assessing urinary para-aminobenzoic acid that is added to all test beverages. After the intervention, participants will ingest a high-fat/high-carbohydrate meal challenge to assess metabolic excursions at 30 min intervals for 3 h. Non-digestible sugar probes also will be ingested prior to collecting 24-h urine to assess region-specific gut permeability. Intervention efficacy will be determined based on circulating endotoxin (primary outcome) and glycemia (secondary outcome). Tertiary outcomes include: gut and systemic inflammatory responses, microbiota composition and short chain fatty acids, gut permeability, and circulating insulin and incretins. Expected Results MFGM is expected to decrease circulating endotoxin and glycemia without altering body mass. These improvements are anticipated to be accompanied by decreased gut permeability, decreased intestinal and circulating biomarkers of inflammation, increased circulating incretins, and beneficial antimicrobial and prebiotic effects in the gut microbiome. Conclusions Demonstration of improvements in gut barrier functions that limit endotoxemia and glycemia could help to establish direct evidence by which full-fat dairy lowers cardiometabolic risk, especially among MetS persons. The clinical trial associated with this paper has been registered at ClinicalTrials.gov, registry number NCT03860584.