Previous studies have shown that individuals with overweight and obesity may experience attentional biases and reduced inhibition toward food stimuli. However, evidence is scarce as to whether the attentional bias is present even before stimuli are consciously recognized. Moreover, it is not known whether or not differences in the underlying brain morphometry and connectivity may co-occur with attentional bias and impulsivity towards food in individuals with different BMIs. To address these questions, we asked fifty-three participants (age M = 23.2, SD = 2.9, 13 males) to perform a breaking Continuous Flash Suppression (bCFS) task to measure the speed of subliminal processing, and a Go/No-Go task to measure inhibition, using food and nonfood stimuli. We collected whole-brain structural magnetic resonance images and functional resting-state activity. A higher BMI predicted slower subliminal processing of images independently of the type of stimulus (food or nonfood, p = 0.001, εp2 = 0.17). This higher threshold of awareness is linked to lower grey matter (GM) density of key areas involved in awareness, high-level sensory integration, and reward, such as the orbitofrontal cortex [t = 4.55, p = 0.003], the right temporal areas [t = 4.18, p = 0.002], the operculum and insula [t = 4.14, p = 0.005] only in individuals with a higher BMI. In addition, individuals with a higher BMI exhibit a specific reduced inhibition to food in the Go/No-Go task [p = 0.02, εp2 = 0.02], which is associated with lower GM density in reward brain regions [orbital gyrus, t = 4.97, p = 0.005, and parietal operculum, t = 5.14, p < 0.001] and lower resting-state connectivity of the orbital gyrus to visual areas [fusiform gyrus, t = -4.64, p < 0.001 and bilateral occipital cortex, t = -4.51, p < 0.001 and t = -4.34, p < 0.001]. Therefore, a higher BMI is predictive of non food-specific slower visual subliminal processing, which is linked to morphological alterations of key areas involved in awareness, high-level sensory integration, and reward. At a late, conscious stage of visual processing a higher BMI is associated with a specific bias towards food and with lower GM density in reward brain regions. Finally, independently of BMI, volumetric variations and connectivity patterns in different brain regions are associated with variability in bCFS and Go/No-Go performances.