In addition to their neurological symptoms, many children and young adults with NCL display severe gastrointestinal problems, although the causes of these symptoms remain unclear. Our recent studies suggest that degeneration of the enteric nervous system (ENS) may be involved. In this study, we examined how altering the gut microbiome affects both central nervous system (CNS) and ENS pathology in a mouse model of CLN2 disease (Tpp1R207X/R207X). Mice received a one-week course of broad-spectrum antibiotics (vancomycin, neomycin, ampicillin, and metronidazole; VNAM) starting after weaning. While VNAM treatment significantly changed the gut microbiota and caused a dramatic and significant reduction in enteric neuron survival in wild-type mice, it did not worsen ENS neurodegeneration in CLN2 mice or the disease-associated pathology that affects intestinal villi and crypt depth and bowel smooth muscle. This suggests that the intestinal abnormalities observed in CLN2 disease are primarily driven by the TPP1 mutation itself rather than by microbiome alterations. Interestingly, VNAM treatment led to a partial reduction in microglial activation in the brains of CLN2 mice, as shown by reduced CD68 immunoreactivity. This unexpected finding hints at a possible link between the gut microbiome and central immune responses. Overall, our results indicate that while the microbiome influences certain aspects of gut and brain physiology, it may not play a major role in driving disease progression in CLN2 disease. These findings offer new insights into gut–brain interactions in the NCLs.