We study quasi-freestanding bilayer graphene on silicon carbide intercalated by calcium. The intercalation, and subsequent changes to the system, were investigated by low-energy electron diffraction, angle-resolved photoemission spectroscopy (ARPES) and density-functional theory (DFT). Calcium is found to intercalate only at the graphene-SiC interface, completely displacing the hydrogen terminating SiC. As a consequence, the system becomes highly n-doped. Comparison to DFT calculations shows that the band dispersion, as determined by ARPES, deviates from the band structure expected for Bernal-stacked bilayer graphene. Instead, the electronic structure closely matches AA-stacked bilayer graphene on calcium-terminated SiC, indicating a spontaneous transition from AB- to AA-stacked bilayer graphene following calcium intercalation of the underlying graphene-SiC interface.