The installation of dynamic photovoltaic panels over apple orchards could meet the challenges of protecting orchards from climate change and drive the energetic transition. However, the impact of solar panel's shading on apple performance needs to be investigated before being commercially adopted. A dynamic agrivoltaic system was installed in the south of France over a 10-year-old 'Golden Delicious' apple orchard and studied during three experimental seasons (2019–2021). This study aimed to evaluate the impact of fluctuating shading (photovoltaic panel orientation to maximise panel light interception) on water relations, leaf morphophysiological characteristics and yield determinants. With the selected photovoltaic design and strategy, trees were grown under a fluctuating shading (variable shading between 4% and 88% during the day) with a mean shading rate of 50–55%. On average, the air temperature was reduced by 3.8 °C, while relative humidity was increased by 14% under shading conditions. Depending on the season, the lower radiation and stressful microclimate decreased the irrigation between 6% and 31%. Fluctuating shading reduced the photosynthetic capacity of leaves and increased their specific leaf area (thinner leaves). The reduction in carbohydrate assimilation under shading was associated with lower starch reserve accumulation in the shoots (-7%), lower flower intensity at the shoot scale (-31%) and a lower proportion of trees with a high floribundity in 2020 (-45%). However, less alternate bearing was observed under shading, and better frost protection resulted in a higher proportion of trees bearing fruit under photovoltaic panels (+31%) and number of fruits per fruit-bearing tree (+44%) in 2021. Fruit size was less sensitive than fruit number to shading. Fruit size was reduced by 17% in 2019 but maintained in 2020 and 2021, probably due to a better water status of shaded trees that accumulated more water. Fruit dry matter content under shading was reduced by an average of 24%. In conclusion, agrivoltaic systems may reduce alternate bearing behaviour in apple trees, showing the importance of carrying out a multi-year study. However, the fluctuating shading strategy tested in this study did not maintain sufficient yields, with yields below 40 t/ha in all three years of study. Identifying the positive and negative effects of shading in this study may be useful for the development of sustainable apple orchard shading strategies.