Insect resistance to toxins derived from Bacillus thuringiensis (Bt) is a major issue in agriculture. Resistance to Bt has been linked to the loss of toxin binding sites within the insect, changes within the gut microbiota, and midgut tissue regeneration. Histopathological documentation of intoxication and resistance to Bt is lacking for rootworms in the genus Diabrotica (Coleoptera: Chrysomelidae), a major target of Bt corn. Here, we document the morphological response of both Bt-resistant and Bt-susceptible larval western corn rootworm, Diabrotica virgifera virgifera LeConte, to intoxication with eCry3.1Ab. Gut lumen structural differences are subtle between the two colonies when feeding on non-Bt corn. However, upon ingestion of Bt-corn roots, susceptible larvae develop symptoms indicative of gut disruption by Bt, whereas resistant larvae incur milder effects. Mild disruption of the peritrophic matrix and gut lumen is accompanied by stem cell proliferation that may lead to midgut tissue regeneration. These results help contextualize the multifaceted nature of Bt-resistance in western corn rootworm for the first time from a histopathological perspective.