Novel approaches have been developed to engineer the microstructure of proton conducting membranes to enhance proton transport. Polymer composite and ceramic membranes were synthesized in which proton conducting pathways are aligned through the plane of the membrane. For polymer composite membranes, electric fields are applied during membrane synthesis to cause proton conducting domains aggregate into connected chains aligned through the membrane. For ceramic membranes, surfactant mediated crystallization is employed to direct crystal growth, resulting in aligned proton conducting paths. For both types of membranes, the engineered microstructure results in significantly enhanced proton conductivity through the membranes and improved performance of the membranes in fuel cells.