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The electronic Seebeck response in a conductor involves the energy-dependent mean free path of the charge carriers and is affected by crystal structure, scattering from boundaries and defects, and strain. Previous photothermoelectric (PTE) studies have suggested that the thermoelectric properties of polycrystalline metal nanowires are related to grain structure, although direct evidence linking crystal microstructure to the PTE response is difficult to elucidate. Here, we show that room temperature scanning PTE measurements are sensitive probes that can detect subtle changes in the local Seebeck coefficient of gold tied to the underlying defects and strain that mediate crystal deformation. This connection is revealed through a combination of scanning PTE and electron microscopy measurements of single-crystal and bicrystal gold microscale devices. Unexpectedly, the photovoltage maps strongly correlate with gradually varying crystallographic misorientations detected by electron backscatter diffraction. The effects of individual grain boundaries and differing grain orientations on the PTE signal are minimal. This scanning PTE technique shows promise for identifying minor structural distortions in nanoscale materials and devices.