Ultra-processed foods expose consumers to heat-induced contaminants like 5-hydroxymethylfurfural (5-HMF), which impairs intestinal homeostasis via oxidative stress and inflammation. This study quantified 5-HMF in bakery products and evaluated blueberry polyphenols’ capacity to attenuate 5-HMF-induced cellular stress in an in vitro Caco-2 intestinal model. 5-HMF levels in commercial bakery products were determined using a colorimetric assay and HPLC-UV. Differentiated Caco-2 cells were exposed to 5-HMF (0.4 mM) for 48 h, alone or co-treated with blueberry juice (15 µg/mL of phenol equivalents). ROS production, lipid accumulation, gene expression of antioxidant, lipid, and inflammatory markers, and NF-κB/ERK signaling pathways were analyzed. HPLC-UV accurately quantified 5-HMF in bakery products (exceeding 2 mg/100 g), revealing systematic overestimation by the colorimetric method. In Caco-2 cells, 5-HMF significantly increased ROS, lipid accumulation, inflammatory cytokines (NLRP3, IL1B, and IL18), and activated NF-κB and p-ERK. Co-treatment with blueberry juice reduced ROS and lipids, upregulated the NRF2 antioxidant pathway, and drastically suppressed NF-κB -mediated inflammation. 5-HMF induced markers of metabolic dysfunction, oxidative stress, and inflammation in the intestinal epithelial model. Polyphenol-rich blueberry juice attenuated 5-HMF-induced alterations at the tested concentration, suggesting a potential protective nutritional strategy against epithelial stress associated with food-processing contaminants.