In rectal cancer, there is a need for improved pretreatment biomarkers applicable to biopsies. Tumor budding (TB) is a histological feature used in colon cancer and, due to its link to epithelial-mesenchymal transition (EMT), is hypothesized to be a potential marker for therapy resistance. As EMT-related processes are also seen in other morphological features beyond TB, we investigated epithelial marker downregulation in tumor tissue, as well as morphological features such as tumor cluster size and finger-like projections. We therefore leveraged five colon cancer images to establish a hyperplex immunofluorescence workflow and a validation cohort consisting of rectal cancer pre-treatment biopsies. We built a custom image analysis pipeline to detect and segment tumor buds and other morphological features and correlated them with molecular expression intensities. We found correlations of epithelial marker downregulation and morphological transition states, both at the invasion front and at the tumor center. We furthermore observed a link between morpho-molecular transitions of nuclear CDX2 expression and tumor cluster size, which in turn informs a novel biomarker. Finally, quantification of these CDX2-based morpho-molecular transition states in rectal biopsies showed that downregulation of CDX2 expression in relation to tumor cluster size is associated with worse disease-free survival.