Control and optimization of optically excited charge and energy transport across solid-liquid interfaces are essential for many applications including artificial photosynthesis, photocatalysis, and photopolymerization. Nanostructures are especially suited for this purpose, because the exciton diffusion length is typically much larger than the dimension of the particle, enabling efficient charge transport from the bulk to the nanoparticle surface for use in chemical transformations. However, characterization of charge transfer processes at nanoscale interfaces involving either isolated or assembled optoelectronic components remains a major challenge. Here, we use conductive probe-atomic force microscopy (cp-AFM) to spatially characterize the photovoltaic and photoelectrochemical properties of individual nanostructured photosynthetically active heterostructure (PAH) units in large area scans and compare them to thin-film photoelectrode devices. For CuInSe2/Au Schottky barrier PAH devices electrochemically synthesized inside porous anodic aluminum oxide, we observed a significant increase in solid-state photovoltages (∼0.5 V) and applied bias photocurrents (∼5 pA at +2 V) with much less spatial variation compared to thin film devices (<0.1 V and ∼2 pA at +2 V). We identified that the key reasons for the low performance of CuInSe2/Au thin film devices were an increased number of short-circuit pathways formed as a result of the fabrication process, and a lower density of grain boundaries leading to reduced photoelectrochemically active surface area. When photoanodes were fabricated with these PAH units, the electrodes showed superior and stable photoelectrochemical performance due to their inherent fault tolerance. Our results demonstrate the potential of using cp-AFM as a tool to characterize spatially resolved photoelectrochemical performance over device structures designed for areal production of chemicals and to provide us with a means of investigating optimal structural configurations and to better understand charge transfer processes across solid-liquid interface.