The coherence of quantum systems is crucial to quantum information processing. While it has been demonstrated that superconducting qubits can process quantum information at microelectronics rates, it remains a challenge to preserve the coherence and therefore the quantum character of the information in these systems. An alternative is to share the tasks between different quantum platforms, e.g. cold atoms storing the quantum information processed by superconducting circuits. In our experiment, we characterize the coherence of superposition states of 87Rb atoms magnetically trapped on a superconducting atom-chip. We load atoms into a persistent-current trap engineered in the vicinity of an off-resonance coplanar resonator, and observe that the coherence of hyperfine ground states is preserved for several seconds. We show that large ensembles of a million of thermal atoms below 350 nK temperature and pure Bose-Einstein condensates with 3.5 x 10^5 atoms can be prepared and manipulated at the superconducting interface. This opens the path towards the rich dynamics of strong collective coupling regimes.