Campylobacter jejuni is the most common cause of foodborne gastroenteritis in humans with about 550 million annual infections worldwide. The extracellular vesicles (EVs) of C. jejuni have an important impact during pathogenicity but their role in invasion of the host intestinal epithelial cells remains largely unknown. In vitro models lack the complexity of tissue and fail to replicate the dynamic interactions between EVs and human intestinal epithelial cells accurately, while animal infection models bring ethical concerns. To bridge this gap, we propose a microfluidic platform integrated with an impedimetric sensor for real-time monitoring of C. jejuni EVs' interaction with human intestinal epithelial cells. When cultured in this microfluidic device, Caco-2 epithelial cells underwent spontaneous 3D morphogenesis and spatially organised in spheroid-like structures. Functional assays revealed that C. jejuni secretome and EVs have a significant cytotoxic effect on Caco-2 cultured on plates. However, 3D Caco-2 spheroids showed increased resistance to the toxicity of secreted virulence factors of C. jejuni. By combining impedance spectroscopy and microscopic observation, the platform allowed real-time monitoring of cellular spatial growth and sensitive detection of the Evs' ability to reach and damage intestinal epithelial cells organised in 3D morphologies. Thus, the developed microfluidic device offers a promising platform for investigating host-microbe interactions and may have a broad impact on biomedical research on gastroenteritis.