The development of patient‐derived intestinal organoids represents an invaluable model for simulating the native human intestinal epithelium. These stem cell‐rich cultures outperform commonly used cell lines like Caco‐2 and HT29‐MTX in reflecting the cellular diversity of the native intestinal epithelium after differentiation. In our recent study examining the effects of polystyrene (PS), microplastics (MPs), and nanoplastics (NPs), widespread pollutants in our environment and food chain, on the human intestinal epithelium, these organoids have been instrumental in elucidating the absorption mechanisms and potential biological impacts of plastic particles. Building on previously established protocols in human intestinal organoid culture, we herein detail a streamlined protocol for the cultivation, differentiation, and generation of organoid‐derived monolayers. This protocol is tailored to generate monolayers incorporating microfold cells (M cells), key for intestinal particle uptake but often absent in current in vitro models. We provide validated protocols for the characterization of MPs/NPs via scanning electron microscopy (SEM) for detailed imaging and their introduction to intestinal epithelial monolayer cells via confocal immunostaining. Additionally, protocols to test the impacts of MP/NP exposure on the functions of the intestinal barrier using transendothelial electrical resistance (TEER) measurements and assessing inflammatory responses using cytokine profiling are detailed. Overall, our protocols enable the generation of human intestinal organoid monolayers, complete with the option of including or excluding M cells, offering crucial techniques for observing particle uptake and identifying inflammatory responses in intestinal epithelial cells to advance our knowledge of the potential effects of plastic pollution on human gut health. These approaches are also amendable to the study of other gut‐related chemical and biological exposures and physiological responses due to the robust nature of the systems. © 2024 Wiley Periodicals LLC.Basic Protocol 1: Human intestinal organoid culture and generation of monolayers with and without M cellsSupport Protocol 1: Culture of L‐WRN and production of WRN‐conditioned mediumSupport Protocol 2: Neuronal cell culture and integration into intestinal epitheliumSupport Protocol 3: Immune cell culture and integration into intestinal epitheliumBasic Protocol 2: Scanning electron microscopy: sample preparation and imagingBasic Protocol 3: Immunostaining and confocal imaging of MP/NP uptake in organoid‐derived monolayersBasic Protocol 4: Assessment of intestinal barrier function via TEER measurementsBasic Protocol 5: Cytokine profiling using ELISA post‐MP/NP exposure.