Cancer stem cells (CSCs) play a crucial role in tumor heterogeneity and the progression of colorectal cancer (CRC). However, identifying and isolating CSCs remains challenging, as conventional methods, such as fluorescent or magnetic labeling, are time-consuming and require substantial technical and biological resources, limiting their clinical applicability. In this study, we evaluated the potential application of a previously established approach with glioma cells, combining sedimentation field-flow fractionation (SdFFF) with a label-free Ultra-High Frequency dielectrophoresis (UHF-DEP) biosensor, for isolating and identifying CRC CSC. The integration of the UHF-DEP biosensor with SdFFF enables the identification of CSCs without specific labeling, simplifying their analysis. To optimize this coupling, we standardized the mobile phase between the two technologies. Producing two CSC sub-populations eluted in Fraction 1 and Fraction 3. For the first time, transcriptomic analysis was employed to deepen our understanding of the genetic composition of the cells, complementing functional and phenotypic characterizations. From these characteristics, it emerged that F1 cells corresponded to precursors, while F3 cells could be considered CSC. The UHF-DEP biosensor demonstrated its ability to detect these differences, linking F3 to cells cultivated in defined medium (DM), used as a reference standard. Finally, transcriptomic analysis (RNA-seq) has deepened our understanding of the genetic profiles of these subpopulations, enriching the interpretation of their characteristics as CSCs. This in-depth approach will also contribute to a better understanding of the results obtained by the UHF-DEP biosensor.