Meningococcal meningitis is a central nervous system infection caused by Neisseria meningitidis, a strictly human pathogen which commonly colonizes the nasopharyngeal epithelium. Antimicrobial peptides (AMPs) are part of the innate immune system and are secreted in response to N. meningitidis ligands recognized primarily by TLR2 and TLR4. This study aimed to investigate expression of the AMPs DEFB1, DEFB4, CAMP and the NF-κB negative regulator TNFAIP3 in hypopharyngeal epithelial FaDu cells exposed to N. meningitidis serogroups B, C, W, Y and the laboratory strain FAM20, and to resolve whether serogroup specific differences in their expression exist. Gene targets were assessed at 24 h post exposure, modelling a sustained response to early nasopharyngeal colonization. Response to commensal Limosilactobacillus reuteri and Ligilactobacillus salivarius bacteria was assessed at 6 h and 24 h as a preliminary comparison. RT-qPCR analysis showed significant upregulation of TNFAIP3 in all live bacterial exposure conditions, with N. meningitidis exposures resulting in high levels of induction. L. salivarius and L. reuteri inductions were modest relative to unexposed controls. DEFB4 was induced in all serogroups at low levels from an undetected baseline. The constitutive expression of DEFB1 became undetectable following exposure to serogroups B, C and W, but not following FAM20 and serogroup Y exposures, possibly indicating serogroup specific suppression. CAMP expression was retained across all exposure conditions. While these findings are consistent with A20 mediated NF-κB attenuation during colonization, no differences between serogroups were significant, suggesting immune response during colonization may depend on ligand structures which vary independently of serogroups.