<p>Intermittent fasting (IF) has gained attention as a potential intervention for cardiometabolic health, though its long-term effects remain unclear. In this randomized clinical trial, we assessed the impact of 6 months of IF on body composition, cardiovascular risk factors, and related molecular pathways in middle-aged (30-65 years) men and women with overweight (BMI 24.8–35 kg/m²). In this trial, 41 participants were randomized to either an intermittent fasting (IF) intervention or to maintain their habitual diet. The primary outcome (circulating CRP concentration) was previously reported; here, we present exploratory analyses focusing on metabolomic and transcriptomic responses. IF led to an 8% reduction in body weight, a 16% decrease in body fat, and significant improvements in lipid profile, including substantial reductions in plasma LDL-cholesterol, non-HDL-cholesterol, and triglycerides (<i>p</i> = 0.001). However, no significant changes were observed in other cardiometabolic risk factors. To investigate the underlying molecular mechanisms, we performed untargeted plasma metabolomics and transcriptomic analysis of colon mucosa biopsies. Significant multi-omic changes were identified, particularly in lipid metabolism, bile acid signaling, and enteroendocrine regulation. Notably, there was a downregulation of transcripts related to glucagon-like peptide 1 (GLP-1) and related enteroendocrine hormones. Correlation analysis highlighted key molecular pathways, with PPAR-α and B-cell-mediated immune processes significantly associated with changes in non-HDL cholesterol. Our findings extend the understanding of IF in humans beyond weight loss, providing key mechanistic insights to inform targeted therapies for improving cardiometabolic health. ClinicalTrials.gov NCT01964118</p>