To date there is an increasing demand for automated cell reprogramming in the fields of cell biology, biotechnology and biomedical sciences. Microfluidic-based platforms that provide unattended manipulation of adherent cells, promise to be an appropriate basis for cell manipulation. In this study we developed a magnetically driven cell carrier to serve as a vehicle within an in-vitro environment. To elucidate the impact of the carrier on the cells, biocompatibility was estimated applying the human adenocarcinoma cell line Caco-2.Besides evaluation of the quality of the magnetic carriers by FE-SEM, the rate of adherence, proliferation, and differentiation of Caco-2 cells grown on the carriers was quantified. Moreover, the morphology of the cells was monitored by immunofluorescent staining. Early generations of the cell carrier suffered from release of cytotoxic nickel from the magnetic cushion. Biocompatibility was achieved by complete encapsulation of the nickel bulk within galvanic gold. The insulation process had to be developed stepwise and was controlled by parallel monitoring of the cell viability. The final carrier generation proved to be a proper support for cell manipulation, providing a proliferative activity of Caco-2 cells equal to glass or polystyrene as a reference for up to 10 days.Functional differentiation was enhanced by more than 30% as compared to the reference. All in all, a flat, ferromagnetic, and fully biocompatible carrier for cell manipulation was developed for application in microfluidic systems. Beyond that, this study offers advice for the development of magnetic cell carriers and the estimation of their biocompatibility.