Agroforestry is promoted as a way to improve the sustainability of horticultural systems through plant diversification and also to mitigate climate change through carbon sequestration. It could also alleviate excessive light and temperature in high-radiation regions of the world. However, little is known about the long-term shade adaptation of the temperate fruit tree in agroforestry systems. A study was developed to investigate apple growing under walnut trees in two shade conditions compared to a full light condition. Our aim was to quantify the plasticity of traits and the covariations between traits in these three light conditions using a multiscale approach considering different scales from whole tree to annual shoot and inflorescence. Shade did not affect the height of the apple trees, while it reduced the diameter of the trunk and branches. On the other hand, the total number of growing shoots was reduced in shade, and flowering and fruiting were fewer and more irregular than in full light. Strikingly, at the whole tree scale, covariations between vegetative traits (trunk cross-sectional area versus mean branch cross-sectional area) and between vegetative and reproductive traits (trunk cross-sectional area versus total number of inflorescences) were not altered by shade. However, at the shoot scale, return-bloom was significantly reduced by shade, whereas at the inflorescence scale shade did not affect leaf number or leaf area. We propose a shade adaptation syndrome that includes not only shade intensity but also shade dynamics during the growing season and over consecutive years.