Micro-solid oxide fuel cells (μ-SOFCs) are fabricated on nanoporous anodic aluminum oxide (AAO) templates with a cell structure composed of a 600-nm-thick AAO free-standing membrane embedded on a Si substrate, sputter-deposited Pt electrodes (cathode and anode) and an yttria-stabilized zirconia (YSZ) electrolyte deposited by pulsed laser deposition (PLD). Initially, the open circuit voltages (OCVs) of the AAO-supported μ-SOFCs are in the range of 0.05 V to 0.78 V, which is much lower than the ideal value, depending on the average pore size of the AAO template and the thickness of the YSZ electrolyte. Transmission electron microscopy (TEM) analysis reveals the formation of pinholes in the electrolyte layer that originate from the porous nature of the underlying AAO membrane. In order to clog these pinholes, a 20-nm thick Al2O3 layer is deposited by atomic layer deposition (ALD) on top of the 300-nm thick YSZ layer and another 600-nm thick YSZ layer is deposited after removing the top intermittent Al2O3 layer. Fuel cell devices fabricated in this way manifest OCVs of 1.02 V, and a maximum power density of 350 mW cm−2 at 500 °C.