In open-canopy ecosystems, thermal imaging affords an unprecedented opportunity to resolve concurrent temperatures of overstory vegetation, understory vegetation, and soil across space and time. This simultaneous view of ecosystem components promises a holistic understanding of ecosystem energy status, defines diverse thermal niches, and can provide a full suite of thermal measurements to drive ecosystem energy budget models. However, thermal imaging in open-canopy ecosystems also presents challenges: emissivity and background radiation data required for image calibration are variable across the scene; mixed pixels can be misleading because of divergent component temperatures; and targets of interest have very different pixel dimensions associated with their different distances from the camera. In this study, we evaluated effects of these challenges on calculated target temperatures, and we contextualized those results with five months of half-hourly thermal images, over vs. understory radiation measurements, ground-based emissivity estimates, and an application of thermal images to drive the two-source energy balance model (TSEB) in a Californian woodland savanna. We found that, though background radiation conditions varied considerably at different locations within the ecosystem, the high emissivities of the ecosystem components minimized the effect of that variation on calibrated target temperatures. Different pixel dimensions (i.e. variable geographical space covered by a single thermal image pixel) were associated with changes of temperature minima and maxima by over one degree Celsius, but they had little effect on aggregate summary values (e.g. estimates of mean temperature). Conversely, mixed pixels, given the relatively widely divergent component temperatures in our heterogeneous system, had the potential to influence calibrated target temperatures dramatically, by several degrees Celsius. The TSEB results corroborate these findings: they are sensitive to differences in component temperatures, while emissivity and reflected radiation corrections result in a negligible difference in sensible heat flux predictions.