The interrelationship between defect chemistry, non-stoichiometry, grain boundary transport and chemical stability of proton conducting perovskites (doped alkaline earth cerates and zirconates) has been investigated. Non-stoichiometry, defined as the deviation of the A : M molar ratio in AMO(3) from 1 : 1, dramatically impacts conductivity, sinterability and chemical stability with respect to reaction with CO2. In particular, alkaline earth deficiency encourages dopant incorporation onto the A-atom site, rather than the intended M-atom site, reducing the concentration of oxygen vacancies. Transport along grain boundaries is, in general, less favorable than transport through the bulk, and thus only in fine-grained materials does microstructure impact the overall electrical properties. The chemical stability of high conductivity cerates is enhanced by the introduction of Zr. The conductivity of BaCe0.9-xZrxM0.1O3 perovskites monotonically decreases with increasing x (increasing Zr content), with the impact of Zr substitution increasing in the order M = Yb --> Gd --> Nd. Furthermore, the magnitude of the conductivity follows the same sequence for a given zirconium content. This result is interpreted in terms of dopant ion incorporation onto the divalent ion site.