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Major cereal yields are expected to decline significantly in coming years due to the effects of climate change temperature rise. Agroforestry systems have been recognized as a useful land management strategy that could mitigate these effects through the shelter provided by trees, but it is unclear how shade affects cereal production. Most cereal species and cultivars have been selected for full light conditions, making it necessary to determine those able to acclimate to low irradiance environments and the traits that drive this acclimation. A greenhouse experiment was conducted in central Spain to assess the photosynthetic response, leaf morphology and grain yield of nine cultivars of winter wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) at three levels of photosynthetic active radiation (100%, 90% and 50%). Cultivars were selected according to three different precocity categories and were widely used in the studied area. The main objective was to assess whether the species and cultivars could acclimate to partial shade through physiological and morphological acclimations and thus increase their grain yield for cultivation in agroforestry systems. Both species increased grain yield by 19% in shade conditions. However, they used different acclimation strategies. Barley mostly performed a physiological acclimation, while wheat had a major morphological adjustment under shaded environment. Barley had lower dark respiration (42%), lower light compensation point (73%) and higher maximum quantum yield (48%) than wheat in full light conditions, revealing that it was a more shade-tolerant species than wheat. In addition, to acclimate to low irradiance conditions, barley showed a 21% reduction of the carotenoids/chlorophyll ratio in the lowest irradiance level compared to 100% light availability and adjusted the chlorophyll a/b ratio, photosystem II quantum efficiency, electron transport rate and non-photochemical quenching to shade conditions. On the other hand, wheat showed a 48% increase in single leaf area in the 50% irradiance level than in full light to maximize light capture. Our results showed that current commercialized wheat and barley cultivars had sufficient plasticity for adaptation to shade, supporting tree presence as a tool to reduce the negative effects of climate change.