We store and control ultra-cold atoms in a new type of trap using magnetic fields of vortices in a high temperature superconducting micro-structure. This is the first time ultra-cold atoms have been trapped in the field of magnetic flux quanta. We generate the attractive trapping potential for the atoms by combining the magnetic field of a superconductor in the remanent state with external homogeneous magnetic fields. We show the control of crucial atom trap characteristics such as an efficient intrinsic loading mechanism, spatial positioning of the trapped atoms and the vortex density in the superconductor. The measured trap characteristics are in good agreement with our numerical simulations.