Honeybee brood biopeptides (HBb-Bps) are a novel source of bioactive compounds with potential health benefits. In this study, HBb-Bps were conjugated with honey via a Maillard reaction and their physicochemical properties, digestive stability, antioxidant capacity, and anti-obesogenic effects were evaluated. Simulated gastrointestinal digestion revealed significantly enhanced resistance after conjugation, with the residual content increasing from 46.99% for native HBb-Bps to 86.12% for the honey-conjugated forms; furthermore, antioxidant activity was largely preserved according to the DPPH and ABTS assays. In the in vivo experiments, 30 male BrlHan: WIST@Jcl (GALAS) (Wistar) rats were fed a high-fat diet (HFD) to induce obesity and orally administered honey-conjugated HBb-Bps at doses of 200, 500, or 1000 mg/kg body weight for 16 weeks. The highest dose led to significant reductions in body weight gain, the Lee index, and body mass index. The serum lipid profiles markedly improved, with decreases in the total cholesterol, triglyceride, and LDL levels, as well as cardiovascular risk indices. Furthermore, fecal analysis showed increased levels of short-chain fatty acids, particularly butyrate. These changes suggest enhanced gut microbial activity; however, the prebiotic effects were inferred from the SCFA profiles, as the gut microbiota composition was not directly analyzed. In conclusion, honey-conjugated HBb-Bps improve gastrointestinal stability and exhibit antioxidant, hypolipidemic, and gut-modulating effects, supporting their potential use as functional ingredients for managing diet-induced metabolic disorders.