Cerebral cavernous malformation (CCM) is a human genetic, cerebrovascular disease that is caused by loss of function mutations in three non-homologous protein coding genes: KRIT1, CCM2, and PDCD10. These proteins form a heterotrimeric CCM adaptor complex that is required in endothelial cells to prevent disease. How loss of this complex causes disease remains unknown. Here, utilizing a neonatal mouse model of disease, we demonstrate that the CCM complex negatively regulates Mitogen-Activated Protein Kinase Kinase Kinase 3 (MAP3K3 aka MEKK3) signaling in endothelial cells. During disease, loss of the CCM complex results in gain of MEKK3 signaling and pathologic overexpression of downstream target transcription factors Kruppel-like Factor 2 and Kruppel-like factor 4 (KLF2 and KLF4). This endothelial MEKK3-KLF2/4 signaling pathway represents the proximal signaling events that are required for lesion formation. If the CCM complex negatively regulates MEKK3 signaling, what are the upstream activators of MEKK3 in the context of disease? We demonstrate that gram-negative bacterial infection and lipopolysaccharide (LPS) activation of endothelial Toll-like receptor 4 (TLR4) drives MEKK3 signaling to stimulate lesion formation. Commensal bacteria in the gut microbiome produce the vast majority of endogenous LPS. We further show through germ-free and broad-spectrum antibiotic experiments, along with 16S fecal analysis of mice spontaneously resistant to lesion formation, that the gram-negative, bacterial microbiome is a primary driver of lesion formation. These studies reveal that endothelial TLR4—MEKK3—KLF2/4 signaling is required for lesion formation and that inhibition of this pathway may be of therapeutic value for CCM patients. They further demonstrate an unexpected role for the gut microbiome in this cerebrovascular disease and suggest that manipulation of host-microbiome interactions may be a viable therapeutic strategy for this lifelong, progressive disease.