The stability of the fast ion conducting cubic phase of zirconia has been investigated using atomistic molecular dynamics to determine the effect of clustering of dopant ions for zirconia containing 11mol% of yttria or scandia stabilizing additive. Large clusters of dopant ions entrap vacancies within the dopant cluster, which increases the average oxygen coordination of the zirconium ions. Not only does this reduce the number of vacancies available for ionic conduction, but it also destabilizes the cubic phase, causing a significant reduction in ionic conductivity as a whole. Using scandia as a stabilizing additive provides better conductivity than yttria, despite the fact that yttria causes a lower coordination for zirconium ions. Cationic migration in the cubic phase occurs too slowly to be captured in molecular dynamics simulations; instead, energy calculations are made, which predict that yttrium dopants exhibit stronger mutually repulsive interactions than scandium ions, which impede the energetically favorable phase segregation process. As a result, aging of yttria stabilized zirconia will proceed at a slower rate than scandia stabilized zirconia. •Studied effect of dopant stratification on scandia- and yttria-stabilized zirconia.•Energy barriers are present in the transition path to stratification.•Nanometer scale precipitates of non-cubic phases can co-exist with the cubic phase.•Energy calculations indicate a preference for a stratified dopant arrangement.