Background Worldwide obesity spread is a global health problem and needs to be further studied. Co-morbidities of obesity include insulin resistance, diabetes mellitus type 2, and dyslipidemia, which are the most frequent contributing factors for metabolic syndrome (MetS), as well as nonalcoholic fatty liver disease and chronic kidney disease. The aim was to study renal function and endogenous intoxication panel on high-calorie diet-induced obesity rat model and perform comparative study of the treatment efficacy of Fenugreek-based bionanocomposite vs antiobesogenic drugs (Orlistat). Materials We included 60 male rats and equally divided them to 6 groups of 10 animals in each group: the experimental groups were firstly assigned as controls and high caloric diet (HCD)-fed groups, and each group further was subdivided to remain untreated, Fenugreek bionanocomposite (BNC)-treated, and Orlistat-treated. Normal control rats (groups 1, 2, 3) were fed by a standard chow, while the others (groups 4, 5, 6) were fed with HCD ad libitum during 98 days. From days 77 to 98, groups 2 and 5 were treated with BNC based on Fenugreek (150 mg/kg body weight, orally) and groups 3 and 6 were treated with antiobesogenic drug Orlistat (10 mg/kg body weight, orally). Food and water consumptions were measured daily and body weights were measured once a week. On day 99, blood was collected; the creatinine, urea, and uric acid were estimated in serum according to the standard protocols. Levels of low and middle molecules (MMs) were measured; the quantity of oligopeptides was estimated by Bradford method. We performed the liver and kidney ultrasonography in rats.Results We revealed an increase in the levels of endogenous intoxication syndrome markers (MM and oligopeptides) in all animals with experimental obesity. Ultrasound data showed injury of the liver and kidneys in obese rats. We observed significant decreasing of MM levels after Orlistat treatment vs controls (p < 0.05). However, this effect was more pronounced in Fenugreek BNC-treated group vs both Orlistattreated and controls (p < 0.05). Orlistat treatment evoked rising of serum creatinine and oligopeptides in control animals