Prebiotics may reduce adiposity and inflammation, improving cognitive function in obese rats, mediated by modulation of the gut-brain axis. Banana-based snacks are promising prebiotic foods. However, their effects on gut microbiota, inflammation, brain reactive oxygen species (ROS) production, microglial morphology, dendritic spine density, and cognitive function remain underexplored in high-fat diet (HFD)-induced obese rats. Seventy-two male rats were maintained on either a normal diet (ND) or a HFD for 16-weeks. At week 13, ND-fed rats were subdivided into six groups (n = 6/group) receiving either a vehicle (NDV, 10.5 mL/kg/day twice daily), prebiotic snacks from bananas at ripening stages 2-5 (NDS2-5, 7.47 g in water, 10.5 mL/kg/day twice daily), or inulin (NDI, 2 g/kg/day in water, 10.5 mL/kg/day twice daily). HFD-fed rats were similarly subdivided into six groups (n = 6/group) with either a vehicle (HFV), banana-based prebiotic snacks (HFS2-5), or inulin (HFI), administered for four weeks at the same doses as the ND-fed rats. HFD-fed rats exhibited both obesity and insulin resistance, gut dysbiosis, inflammation, and cognitive impairment. However, rats receiving inulin or banana-based prebiotics from all ripening stages exhibited improved cognitive function by reducing gut dysbiosis, oxidative stress, inflammation, brain ROS, apoptosis, dendritic spine loss, and microglial activation. Prebiotic banana snacks from all ripening stages may protect against HFD-induced cognitive impairment by enhancing gut health and reducing inflammation and oxidative stress, potentially via the gut-brain axis. These findings support their potential use as functional foods to promote both cognitive and metabolic health.