Leaf reflectance spectral measurements are an emerging non-invasive technique that can be used to derive the photochemical reflectance index (PRI) to assess the physiological state of plants from leaf to ecosystem level. Changes in PRI are associated with changes in the xanthophyll cycle activity and provide an estimate of changes in the effective photochemical quantum efficiency (Φ_II) during the growing season. However, we hypothesised that the correlation between PRI and Φ_II might be poor when the xanthophyll cycle is primed for sustained thermal dissipation of the light energy absorbed. To test our hypothesis, we studied the recovery of winter acclimated Jack pine (Pinus banksiana Lamb.) seedlings that were exposed to different simulated spring recovery treatments in controlled environments. Different growth temperatures and light intensities were used to dissect the effect of these two factors on chlorophyll fluorescence, pigment composition and leaf reflectance. Φ_II showed a clear response to temperature whereas PRI was mostly affected by light intensity. In contrast, the de-epoxidation state of the xanthophyll cycle pigments was both temperature and light dependent. Our data suggest that zeaxanthin-independent non-photochemical quenching is employed to various degrees in the different treatments. As a result, within the limits of our experimental setup, PRI could not explain the variation in Φ_II. This indicates that an improved understanding of the different energy quenching mechanisms is critical to accurately interpret the PRI signal under environmental conditions where the predominant mode of excess energy dissipation does not involve a dynamic operation of the xanthophyll cycle, but a sustained mechanism of energy dissipation.