Under land and climate change scenarios, agriculture has experienced water competitions among other sectors in the São Paulo state, Brazil. On the one hand, in several occasions, in the northeastern side of this state, nowadays sugar-cane is expanding, while coffee plantations are losing space. On the other hand, both crops have replaced the natural vegetation composed by Savannah and Atlantic Coastal Forest species. Under this dynamic situation, geosciences are valuable tools for evaluating the large-scale energy and mass exchanges between these different agro-ecosystems and the lower atmosphere. For quantification of the energy balance components in these mixed agro-ecosystems, the bands 1 and 2 from the MODIS product MOD13Q1 were used throughout SAFER (Surface Algorithm for Evapotranspiration Retrieving) algorithm, which was applied together with a net of 12 automatic weather stations, during the year 2015 in the main sugar cane and coffee growing regions, located at the northeastern side of the state. The fraction of the global solar radiation (RG) transformed into net radiation (Rn) was 52% for sugar cane and 53% for both, coffee and natural vegetation. The respective annual fractions of Rn used as λE were 0.68, 0.87 and 0.77, while for the sensible heat (H) fluxes they were 0.27, 0.07 and 0.16. From April to July, heat advection raised λE values above Rn promoting negative H, however these effects were much and less strong in coffee and sugar cane crops, respectively. The smallest daily Rn fraction for all agro-ecosystems was for the soil heat flux (G), with averages of 5%, 6% and 7% in sugar cane, coffee and natural vegetation. From the energy balance analyses, we could conclude that, sugar-cane crop presented lower annual water consumption than that for coffee crop, what can be seen as an advantage in situations of water scarcity. However, the replacement of natural vegetation by sugar cane can contribute for warming the environment, while when this occur with coffee crop there was noticed cooling conditions. The large scale modeling satisfactory results confirm the suitability of using MODIS products together with weather stations to study the energy balance components in mixed agro-ecosystems under land-use and climate change conditions.