Paramagnetic defects of thin CaO(001) films grown on Mo(001) are characterized using electron paramagnetic resonance (EPR) spectroscopy under ultrahigh vacuum conditions. A variety of paramagnetic centers located in the volume of the films are identified whose speciation as well as relative abundance was found to depend on the growth rate of the films. Pristine films prepared at a lower growth rate exhibited a larger number and a different speciation of paramagnetic defects than films grown at a higher rate. Annealing of the films to 1030 K, which improves their long-range order, results in quenching of most of the paramagnetic species observed for the pristine film; however, films prepared at a lower growth rate exhibit new paramagnetic signals upon annealing, which are absent in films prepared at a higher growth rate. The signals can be assigned to paramagnetic Mo ions previously shown to diffuse into these films. These results indicate that the amount and speciation of the transition metal ions depend on the preparation conditions which in turn can also affect the surface chemistry of these systems.