Background: Manganese oxide has been shown to cause toxicity and is associated with occupational-related disease (e.g., welders). With the goal to improve several biomedical areas, manganese oxide nanoparticles (MnO NP) are being considered for use in drug delivery and magnetic resonance imaging (MRI) to obtain high resolution anatomical images of tumors and gastrointestinal (GI) inflammation. Regardless of whether it is intentional or unintentional ingestion, the GI tract has been shown to be the primary route of entry for metal nanoparticles including MnO NP. However, studies assessing toxicity of MnO NP for intestinal epithelial cells (IECs) are virtually nonexistent. Methods: Given the proximity to the GI lumen, assessing the effects of nanoparticles on IECs in the presence of bacterial components presents a more holistic model of exposure. Therefore, we examined the effects of MnO NP alone and MnO NP in combination with Escherichia coli LF82 bacterial lysate on selected functions of MODE-K cells, a murine intestinal epithelial cell line. Data were analyzed using one-way ANOVA. Differences with p < 0.05 were considered significant. Results: Results showed MnO NP plus E. coli LF82 lysate added to MODE-K cells severely inhibited monolayer scratch wound healing, enhanced the secretion of interleukin 6 (IL-6), and induced mitochondrial dysfunction. Conclusions: Overall, our findings show that toxicity of MnO NP deleteriously affected MODE-K cells and demonstrated the necessity to integrate other environmental factors, such as microbial components and/or inflammatory cytokines, into studies assessing effects of nanoparticles on mucosal epithelia.