Abstract. The thermal-based Two-Source Energy Balance (TSEB) model has successfully simulated energy fluxes in a wide range of landscapes. However, tree-grass ecosystems (TGE) have notably complex heterogenous vegetation mixtures and dynamic phenological characteristics presenting clear challenges to earth observation and modeling methods. Therefore, the TSEB model was adapted here to consider these significant seasonal changes. To ensure this and understand model dynamics, sensitivity analyses (SA) were conducted on both inputs (local SA) and parameters (global SA). Furthermore, a more physically based wind attenuation sub-model was applied and compared against the classical exponential wind attenuation law. The model was subsequently modified (TSEB-2S) and evaluated against eddy covariance (EC) flux measurements and lysimeters over a TGE experimental site in central Spain. TSEB-2S vastly improved modeled fluxes decreasing the mean bias and RMSD of LE from 34 and 77 W m^-2 to 4 and 56 W m^-2, respectively during 2015. TSEB-2S was further validated for two other EC towers and for different years (2015, 2016 and 2017) obtaining similar error statistics. The results presented here demonstrate the important role that vegetation, through its structure and phenology, has in controlling ecosystem level energy fluxes, which become important considerations for the modeling procedure. Additionally, TSEB showed to be more sensitive to correctly partitioning incoming radiation, such as characterizing vegetation clumping, compared to accurately modeling the wind profile through the canopy or the aerodynamic roughness.