The present paper aims at investigating how changes in canopy structure and species physiology associated with the abandonment of mountain meadows and pastures affect their net photosynthesis. For this purpose, a multi-layer vegetation–atmosphere transfer (VAT) model is employed, which explicitly takes into account the structural and functional properties of the various canopy components and species. Three sites differing in land use are investigated, a meadow, a pasture and an abandoned area. Model simulations agree reasonably with measured canopy net photosynthetic rates, the meadow featuring the highest daily net photosynthesis, followed by the pasture and, finally, the abandoned area. A detailed process analysis suggests this ranking to be mainly due to bulk canopy physiology, which decreases from the meadow to the pasture and the abandoned area, reflecting species composition and species-specific photosynthetic capacities. Differences between the canopies with regard to canopy structure are found to be of minor importance. The amounts of green, photosynthetically active plant matter are too similar at the three sites to be a major source of variation in net photosynthesis. Large differences exist between the canopies with regard to the amount of photosynthetically inactive phytoelements. Even though a model analysis showed them to be potentially important, most of them are accumulated close to the ground surface, where they exert little influence on canopy net photosynthesis.