Mixed ionic and electronic conducting (MIEC) films can be applied in solid state electrochemical devices such as oxygen separation membranes for producing pure oxygen, gas sensors or as cathode in solid oxide fuel cells. The current interest in layered perovskite-related phases, like Sr4Fe6O13 (SFO), arises from their significant oxygen permeability as predicted from theoretical studies. Nevertheless, before any practical application further fundamental study on this fairly unknown oxide is required mainly to assess the mechanisms affecting the transport properties. Epitaxial Sr4Fe6O12+δ (SFO) films of b-axis orientation with different thicknesses have been prepared by the pulsed laser deposition technique onto different perovskite substrates: SrTiO3, NdGaO3 and LaAlO3. The strain accommodation has been found to vary as a function of film thickness as well as the substrate material causing different type of defects in the film microstructure, as well as variations in the oxygen anion content and ordering. Correspondingly, the total electrical conductivity of the films has been also found to vary significantly as a function of thickness and substrate type showing an unexpected enhancement for strained thin films. The variations in the transport properties are discussed in terms of the different strain accommodation mechanisms and the variation of the modulated structure observed for this compound.