Here, we report a synthetic strategy to control the B-site ordering of the transition metal-doped perovskite-type oxides with the nominal formula of BaCa(0.335)M(0.165)Nb(0.5)O(3-δ) (M = Mn, Fe, Co). Variable temperature (in situ) and ex situ powder X-ray diffraction (PXRD), selected area electron diffraction (SAED), energy dispersive X-ray spectroscopy (EDX), Fourier transform infrared spectroscopy (FTIR), scanning/transmission electron microscopy (SEM/TEM), and thermogravimetic analysis (TGA) were used to understand the B-site ordering as a function of temperature. The present study shows that BaCa(0.335)M(0.165)Nb(0.5)O(3-δ) crystallizes in the B-site disordered primitive perovskite (space group s.g. Pm3̅m) at 900 °C in air, which can be converted into the B-site 1:2 ordered perovskite (s.g. P3̅m1) at 1200 °C and the B-site 1:1 ordered perovskite phase (s.g. Fm3̅m) at 1300 °C. However, the reverse reaction is not feasible when the temperature is reduced. FTIR revealed that no carbonate species were present in all three polymorphs. The chemical stability of the investigated perovskites in CO2 and H2 highly depends on the B-site cation ordering. For example, TGA confirmed that the B-site disordered primitive perovskite phase is more readily reduced in dry and wet 10% H2/90% N2 and is less stable in pure CO2 at elevated temperature, compared to the B-site 1:1 ordered perovskite-type phase of the same nominal composition.