The tumor microbiome has been implicated in pancreatic ductal adenocarcinoma (PDAC)’s poor response to treatment, demanding new methods for understanding host-microbe interactions in therapy. Traditional 2D systems, while widely used, fail to adequately recapitulate human PDAC due to insufficient representation of structural, immunological and stromal components. Differences in cancer-specific microbiomes, microbe-immune interactions, and the unique physiological and immunosuppressive features of PDAC have hindered the clinical translation of immune therapies. Reproducible 3D culture systems that integrate the human tumor–immune–microbe axis represent a promising avenue for treatment research, yet they remain underexplored in PDAC. In this narrative review, we discuss the key microbial determinants of therapy resistance in PDAC, explore the current 3D multi-cellular modelling approaches in other cancer types, and provide a path forward for similar integrative translational models in PDAC.