Summary Leaves are built from multiple cell types and are structured to enable the conversion of carbon dioxide and water into sugars in the process of photosynthesis. Understanding how cell architecture impacts the movement of CO 2 within leaves may provide means to improve photosynthesis. Here, we examined the impact of mesophyll cell architecture on air networks and air permeability by employing high‐resolution tomography data in leaves of Arabidopsis thaliana wild‐type plants and in plants with altered Rho of Plant (ROP)‐GTPase‐related activities. We employed high‐resolution tomography to characterise leaf cell architecture and associated air space networks. The image data were segmented and analysed using machine learning, and combined with leaf gas exchange measurements to evaluate photosynthesis‐related traits. We found that changes in the ROP‐GTPase pathway substantially altered the leaf cell architecture, causing disruptions in the air space network associated with higher tortuosity. In addition, changes in ROP‐GTPase activity resulted in reduced mesophyll conductance. Our observations underscore how changes in leaf cell architecture potentially drive alterations in photosynthesis‐related traits, highlighting a mechanistic link between mesophyll geometry, air space organisation, and CO 2 diffusion.