We propose a novel and robust technique to realize a beam splitter for trapped Bose-Einstein condensates (BECs). The scheme relies on the possibility of producing different potentials simultaneously for two internal atomic states. The atoms are coherently transferred, via a Rabi coupling between the two long-lived internal states, from a single well potential to a double-well. We present numerical simulations supporting our proposal and confirming excellent efficiency and fidelity of the transfer process with realistic numbers for a BEC of 87Rb. We discuss the experimental implementation by suggesting state-selective microwave (MW) potentials as an ideal tool to be exploited for magnetically trapped atoms. The working principles of this technique are tested on our atom chip device which features an integrated coplanar MW guide. In particular, the first realization of a double-well potential by using a MW dressing field is reported. Experimental results are presented together with numerical simulations, showing good agreement. Simultaneous and independent control on the external potentials is also demonstrated in the two Rubidium clock states. The transfer between the two states, featuring respectively a single and a double-well, is characterized and it is used to measure the energy spectrum of the atoms in the double-well. Our results show that the spatial overlap between the two states is crucial to ensure the functioning of the beamsplitter. Even though this condition could not be achieved in our current setup, the proposed technique can be realized with current state-of-the-art devices being particularly well suited for atom chip experiments. We anticipate applications in quantum enhanced interferometry.