Bioinsecticides made of the bacterium Bacillus thuringiensis (Bt) are the bioinsecticide best sale worldwide. Due to the governmental policies and the public opinion, the use of such products has increased exponentially over the last decade. Among Bt bioinsecticides, those based on the strain Bt var. kurstaki (Btk) are widely used in farming to fight lepidopteran pests. Although there is much evidence of the short-term safety of Btk products on non-target animals, only scarce data are available on their long-term unintended effects. Here, we aimed to characterize the putative unintended effects of the ingestion of environmental doses of Btk products on the larval development of the non-target dipteran Drosophila melanogaster. We showed that Btk products impair growth and developmental time of Drosophila larvae. These effects are mediated by the synergism between Btk bacteria and Btk insecticidal toxins, which induces significant apoptosis of enterocytes, resulting in a decreased intestinal capacity to digest proteins. The harmful effects can be compensated by a protein-rich diet or the addition of the probiotic bacterium Lactobacillus plantarum in the food. Finally, we uncovered the ability of the larval midgut to maintain its integrity upon Btk aggression thanks to both the generation of new immature cells arising from adult midgut precursors and the flattening of old enterocytes. Our work demonstrates that unintended effects of Btk products impede gut physiology but can be mitigated by the regenerative capacity of the gut, the commensal flora composition and the diet composition.