Phase composition, degree of cation ordering, and dielectric properties of complex perovskites with general formula Ba(B' 1/3B"2/3)O3, where B′ = Mg, Zn, and Ni and B" = Nb and Ta, were analyzed. It was found that all the studied complex perovskites attained high degrees of 1:2 cation ordering at temperatures specific to each composition. A high temperature order–disorder phase transition in Ba(Zn1/3Nb2/3)O3 occurred below 1380 °C. Ba(Ni1/3Nb2/3)O3 (BNN) and Ba(Mg1/3Nb2/3)O3 (BMN) pervoskites remained 100% ordered at temperatures as high as 1500 and 1620 °C, respectively. It was found that in BMN and BNN extrinsic factors, such as the second phase (i.e., Ba3Nb5O15) and point defects, dominated the dielectric loss at microwave frequencies. Ba(Mg1/3Ta2/3)O3 (BMT) remained single phase up to 1630 °C. Above this temperature, the Ba3Ta5O15 second phase was detected. A decrease in the 1:2 cation ordering and increase of dielectric loss in BMT occurred at sintering temperatures above 1590 °C. It was also revealed by electron paramagnetic resonance that all samples studied contained a substantial amount of paramagnetic point defects. These defects contributed to extrinsic dielectric loss at microwave frequencies, thus degrading the Q factor.