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This paper discusses microwave-induced electroporation as a promising alternative to conventional transfection methods. Adherent C2C12 mouse cells are successfully transfected with a 5TAMRA redlabeled peptide by using a recently developed planar microwave electroporation tool. It allows to monitor the uptake kinetics with live-cell confocal microscopy and is suitable to culture, manipulate, and observe the adherent cells over several days. Viability tests with the Calcein blue AM proof the vitality of the treated cells after 72 h. The question of whether the observed effects are temperature or field induced is tackled. For this reason, comprehensive coupled full-wave electromagnetic-thermal simulations are aligned with temperature measurements. The temperature at the position of the cells does not exceed 34 °C for an input power of 24 dBm. The corresponding electric field strength is evaluated at the position of the cells. A value of 150 V/cm is not exceeded, which is at least a factor of 10 below the field strength of the conventional electroporation. Consequently, almost no cell mortality does occur during the treatment. Comparative thermal tests without a microwave field but with a successively increased temperature up to 42 °C show no uptake. In contrast, the successful uptake follows the pattern of the microwave field although the temperature distribution is homogeneous. We rate this as evidence that the uptake is induced by the high-frequency electromagnetic field rather than the temperature.