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Simple Summary: Pancreatic ductal adenocarcinoma (PDAC) is characterized by high tumor cell plasticity and heterogeneity, contributing to poor prognosis and treatment failure. Epithelial–mesenchymal transition (EMT) and gain of cancer stem cell (CSC) properties are crucial processes determining tumor cell plasticity. Investigating CSC and non-CSC clones from PDAC cell lines revealed that epithelial and mesenchymal-like CSCs are characterized by different self-renewal abilities and metastatic propensities. Epithelial CSCs were characterized by the expression of the CSC marker SOX2, fast cell growth, and strong self-renewal ability in vitro, together with massive tumor formation in vivo. In contrast, mesenchymal-like CSCs showed a strong expression of the CSC marker Nestin, slower cell growth, self-renewal ability in vitro, and the formation of higher numbers of smaller tumors in vivo. Furthermore, the organ manifestation of mesenchymal-like and epithelial CSC-derived tumors clearly differed. Thus, this study revealed that CSC and non-CSC populations in PDAC can be associated with distinct EMT phenotypes, resulting in distinct metastatic behavior. Pancreatic ductal adenocarcinoma (PDAC) is mostly diagnosed at advanced or even metastasized stages, limiting the prognoses of patients. Metastasis requires high tumor cell plasticity, implying phenotypic switching in response to changing environments. Here, epithelial–mesenchymal transition (EMT), being associated with an increase in cancer stem cell (CSC) properties, and its reversion are important. Since it is poorly understood whether different CSC phenotypes exist along the EMT axis and how these impact malignancy-associated properties, we aimed to characterize CSC populations of epithelial and mesenchymal-like PDAC cells. Single-cell cloning revealed CSC (Holoclone) and non-CSC (Paraclone) clones from the PDAC cell lines Panc1 and Panc89. The Panc1 Holoclone cells showed a mesenchymal-like phenotype, dominated by a high expression of the stemness marker Nestin, while the Panc89 Holoclone cells exhibited a SOX2-dominated epithelial phenotype. The Panc89 Holoclone cells showed enhanced cell growth and a self-renewal capacity but slow cluster-like invasion. Contrarily, the Panc1 Holoclone cells showed slower cell growth and self-renewal ability but were highly invasive. Moreover, cell variants differentially responded to chemotherapy. In vivo, the Panc1 and Panc89 cell variants significantly differed regarding the number and size of metastases, as well as organ manifestation, leading to different survival outcomes. Overall, these data support the existence of different CSC phenotypes along the EMT axis in PDAC, manifesting different metastatic propensities. [ABSTRACT FROM AUTHOR]