We present cavity QED experiments with an Er3+:Y2SiO5 crystal magnetically coupled to a three-dimensional (3D) cylindrical sapphire loaded copper resonator. Such waveguide cavities are promising for the realization of a superconducting quantum processor. Here, we demonstrate the coherent integration of a rare-earth spin ensemble with the 3D architecture. The collective coupling strength of the Er3+ spins to the 3D cavity is 21 MHz. The cylindrical sapphire loaded resonator allowed us to explore the anisotropic collective coupling between the rare-earth doped crystal and the cavity. This work shows the potential of spin doped solids in 3D quantum circuits for application as microwave quantum memories as well as for prospective microwave to optical interfaces.