The Western US accounts for a significant amount of the forested biomass and carbon uptake within the conterminous United States. Warming and drying climate trends combined with a legacy of fire suppression have left Western forests particularly vulnerable to disturbance from insects, fire and drought mortality. These challenging conditions may significantly weaken this region’s ability to uptake carbon from the atmosphere and warrant continued monitoring. Traditional methods of carbon monitoring are limited by the complex terrain of the Rocky Mountains that lead to complex atmospheric flows coupled with heterogeneous climate and soil conditions. Recently, solar induced fluorescence (SIF) has been found to be a strong indicator of GPP, and with the increased availability of remotely-sensed SIF, provides an opportunity to estimate GPP and ecosystem function across the Western US. Although the SIF-GPP empirical linkage is strong, the mechanistic understanding between SIF and GPP is lacking, and ultimately depends upon changes in leaf chemistry that convert absorbed radiation into photochemistry, heat (via non-photochemical quenching (NPQ)), leaf damage or SIF. Understanding of the mechanistic detail is necessary to fully leverage observed SIF to constrain model estimates of GPP and improve representation of ecosystem processes. Here, we include an improved fluorescence model within CLM 4.5 to simulate seasonal changes in SIF at a sub-alpine forest in Colorado. We find that when the model includes a representation of sustained NPQ the simulated fluorescence is much closer to the seasonal pattern of SIF observed from the GOME-2 satellite platform and a custom tower mounted spectrometer system. We also find that average air temperature may be used as a predictor of sustained NPQ when observations are not available. This relationship to air temperature is promising because it may allow for efficient spatial upscaling of SIF simulations, given widespread availability of temperature data, but not NPQ observations. Further improvements to the fluorescence model should focus upon distinguishing between the impacts of NPQ versus the de-activation of photosystems brought on by high-stress environmental conditions.