Micromachined fuel cells are among a class of microscale devices being explored for portable power generation. In this paper, we report processing and geometric design criteria for the fabrication of free-standing electrolyte membranes for microscale solid-oxide fuel cells. Submicron, dense, nanocrystalline yttria-stabilized zirconia (YSZ) and gadolinium-doped ceria (GDC) films were deposited onto silicon nitride membranes using electron-beam evaporation and sputter deposition. Selective silicon nitride removal leads to free-standing, square, electrolyte membranes with side dimensions as large as 1025 μm for YSZ and 525 μm for GDC, with high processing yields for YSZ. Residual stresses are tensile (+85 to +235 MPa) and compressive (–865 to -155 MPa) in as-deposited evaporated and sputtered films, respectively. Tensile evaporated films fail via brittle fracture during annealing at temperatures below 773 K; thermal limitations are dependent on the film thickness to membrane size aspect ratio. Sputtered films with compressive residual stresses show superior mechanical and thermal stability than evaporated films. Sputtered 1025-μm membranes survive annealing at 773 K, which leads to the generation of tensile stresses and brittle fracture at elevated temperatures (923 K).