Evapotranspiration (ET) is a key variable in the hydrological cycle and it directly impacts the surface balance and its accurate assessment is essential for a correct water management. ET is difficult to measure, since the existing methods for its direct estimate, such as the weighing lysimeter or the eddy-covariance system, are often expensive and require well-trained research personnel. To overcome this limit, different authors developed experimental models for indirect estimation of ET. However, since the accuracy of ET prediction is crucial from different points of view, the continuous search for more and more precise modeling approaches is encouraged. In light of this, the aim of the present work is to test the efficiency in predicting ET fluxes in a newly introduced physical-based model, named Prospero, which is based on the ability to compute the ET using a multi-layer canopy model, solving the energy balance both for the sunlight and shadow vegetation, extending the recently developed Schymanski and Or method to canopy level. Additionally, Prospero is able to compute the actual ET using a Jarvis-like model. The model is integrated as a component in the hydrological modelling system GEOframe. Its estimates were validated against observed data from five Eddy covariance (EC) sites with different climatic conditions and the same vegetation cover. Then, its performances were compared with those of two already consolidated models, the Priestley–Taylor model and Penman FAO model, using four goodness-of-fit indices. Subsequently a calibration of the three methods has been carried out using LUCA calibration within GEOframe, with the purpose of prediction errors. The results showed that Prospero is more accurate and precise with respect to the other two models, even if no calibrations were performed, with better performances in dry climatic conditions. In addition, Prospero model turned to be the least affected by the calibration procedure and, therefore, it can be effectively also used in a context of data scarcity.