Ba3CaNb2O9 is a 1:2 ordered perovskite which presents a trigonal cell within the D3d3space group. Dense ceramics of Ba3CaNb2O9 were prepared by the solid-state reaction route, and their microwave dielectric features were evaluated as a function of the sintering time. From Raman spectroscopy, by using group-theory calculations, we were able to recognize the coexistence of the 1:1 and 1:2 ordering types in all samples, in which increasing the sintering time tends to reduce the 1:1 domain, leading to an enhancement of the unloaded quality factor. We concluded that this domain acts as a lattice vibration damping, consequently raising the dielectric loss at microwave frequencies. The best microwave dielectric parameters were determined in ceramics sintered at 1500 °C for 32h: ε′ ~ 43; Qu×fr = 15,752 GHz; τf ~ 278 ppm °C−1.