The Brazilian Cerrado biome is known for its high biodiversity, and the role of groundwater recharge and climate regulation. Anthropogenic influence has harmed the biome, emphasizing the need for science to understand its response to climate and reconcile economic exploration with preservation. Our work aimed to evaluate the seasonal and interannual variability of the surface energy balance in a woodland savanna (Cerrado) ecosystem in southeastern Brazil over a period of 19 years, from 2001 to 2019. Using field micrometeorological measurements, we examined the variation in soil moisture and studied its impact on the temporal pattern of energy fluxes to distinguish the effects during rainy years compared to a severe drought spell. The soil moisture measures used two independent instruments, cosmic ray neutron sensor CRNS, and FDR at different depths. The measures were taken at the Pé de Gigante (PEG) site, in a region of well-defined seasonality with the dry season in winter and a hot/humid season in summer. We gap-filled the energy flux measurements with a calibrated biophysical model (SiB2). The long-term averages for air temperature and precipitation were 22.5 °C and 1309 mm/year, respectively. The net radiation (Rn) was 142 W/m2, the evapotranspiration (ET) and sensible heat flux (H) were 3.4 mm/d and 52 W/m2, respectively. Soil moisture was marked by a pronounced negative anomaly in the 2014 year, which caused an increase in the Bowen ratio and a decrease in Evaporative fraction, that lasted until the following year 2015 during the dry season, despite the severe meteorological drought of 2013/2014 already ending, which was corroborated by the two independent measurements. The results showed the remarkable influence of precipitation and soil moisture on the interannual variability of the energy balance in this Cerrado ecosystem, aiding in understanding how it responds to strong climate disturbances.