Agrivoltaics (APV) systems, integrating solar energy generation with agriculture, offer a promising solution for optimizing land use facing a rising energy demand and climate change concerns. However, the impact of APV induced shading on orchards micrometeorology and physiology is not fully understood. This study investigated the effects of simulated APV shading on sensible heat flux, temperature, humidity, wind, CO₂ flux, and evapotranspiration (ET) in deciduous plum and nectarine orchards in northern Israel. Using the eddy covariance (EC) method, we measured CO₂ and water vapor fluxes in adjacent shaded and unshaded (referred to as ‘paneled’ and ‘sunlit’) sections. Principal component analysis (PCA) and linear regression were employed to analyze the relationships between meteorological variables and the measured fluxes. Results showed significantly higher rates of CO₂ flux (absorption) and ET in the paneled sections compared to sunlit sections, particularly during summer peak radiation hours. These findings suggest that partial shading moderates environmental stress (excessive heat, high vapor pressure deficit), improving stomatal function, enhancing photosynthesis, and potentially promoting water use efficiency. This research integrates the EC method with APV system analyses in orchards, providing novel insights into the dynamic interactions under shading and highlighting the potential of APV to enhance agricultural sustainability in semi-arid climates.