The correct estimation of Sensible Heat Flux (H) and Latent Heat Flux (LE) (i.e., turbulent fluxes) is vital in the understanding of exchange of energy and mass among hydrosphere, atmosphere, and biosphere in an ecosystem. One of the most popular methods to measure these fluxes is the Eddy Covariance (EC) technique; however, there are a number of setbacks to its application, especially in remote and topographically complex terrain such as the higher altitudes of the Andes. Efforts have been made by the scientific community to parameterise these fluxes based on other more commonly measured variables. One of the most widespread methods is the so-called bulk method, which relates average temperature, humidity, and wind vertical profiles to the turbulent fluxes. Another approach to estimate LE is the Penman-Monteith (PM) equation which uses meteorological measurements at a single level. The objective of this study was to validate these methods for the first time in the Tropical Andes in Southern Ecuador (in the paramo ecosystem at 3780 m a.s.l.) using EC and meteorological measurements. It was determined that the bulk method was the best to estimate H, although some adjustments had to be made to the typical assumptions used to estimate surface meteorological values. On the other hand, the PM equation yielded the best LE estimations. For both fluxes, the error in the estimations was within the uncertainty range of the EC measurements. It can be concluded that it is possible to accurately estimate H and LE using the methods described in this paper in this ecosystem when no direct measurements are available.