The effect of electric field assisted annealing on the microstructure, composition and ionic conductivity properties in CeO2/YSZ oxide heterostructures have been investigated using molecular dynamics simulations. Amorphization–recrystallization steps were performed with and without external electric field of strength 10 MV/cm along three different orientations: in-plane (YZ), normal (X) and 45° resultant (XY) with respect to the oxide heterointerfaces. The microstructural and compositional differences at the interfaces and in the interior of the oxide heterolayers were evaluated and were found to show a clear correlation with the orientations of the applied field. In particular, the XY configuration displayed a compressive lattice strain of ∼9% along with a reduced oxygen vacancy concentration when compared to the others. Ionic density profiles suggest pronounced segregation (∼60% higher compared to the average value in the interior) of yttrium ions closer to the YSZ/CeO2 interface for the XY configuration. Other configurations exhibit minimal to no such variations. These microstructural differences are found to affect the number of mobile charge carriers and the activation barriers associated with ionic migration through the oxide lattice and consequently, influence the ionic conductivity.