Increasing vegetation cover in cities is a key approach to mitigating urban heat excess. However, both the effect of vegetation on microclimate and the plants’ vitality need to be assessed to support and quantify the effects of such strategies. One way to assess the interactions between vegetation and the urban environment is through microclimate models that can simulate the effects of vegetation onto the urban microclimate as well as effects of urban environments onto vegetation. To provide reliable estimates microclimate models need to be parameterized based on empirically obtained data. In this paper we compare modeled transpiration rates and leaf temperatures of a leading microclimate model, ENVI-met V4, with in-situ measured stem sap flow and leaf temperatures of two different trees in an urban courtyard. The vegetation model of ENVI-met is evaluated considering four synoptic situations including varying cloud covers ranging from fully cloudy to clear sky. The comparison of simulation results with empirical data reveals a high agreement. The model is capable of capturing the magnitude as well as short-term variations in transpiration caused by microclimatic changes. However, substantial deviations were found in situations with low photosynthetic active radiation. Modeled and observed diurnal tree transpiration and leaf temperature showed good agreement. These findings indicate that ENVI-met is capable of simulating transpiration rates and leaf temperatures of trees in complex urban environments.