Global atmospheric models rely on parameterizations to capture the effects of gravity waves (GWs) on middle atmosphere circulation. As they propagate upwards from the troposphere, the momentum fluxes associated with these waves represent a crucial yet insufficiently constrained component. The present study employs three tree‐based ensemble machine learning (ML) techniques to probe the relationship between large‐scale flow and small‐scale GWs within the tropical lower stratosphere. The measurements collected by eight superpressure balloons from the Strateole 2 campaign, comprising a cumulative observation period of 680 days, provide valuable estimates of the gravity wave momentum fluxes (GWMFs). Multiple explanatory variables, including total precipitation, wind, and temperature, were interpolated from the ERA5 reanalysis at each balloon's location. The ML methods are trained on data from seven balloons and subsequently utilized to estimate reference GWMFs of the remaining balloon. We observed that parts of the GW signal are successfully reconstructed, with correlations typically around 0.54 and exceeding 0.70 for certain balloons. The models show significantly different performances from one balloon to another, whereas they show rather comparable performances for any given balloon. In other words, limitations from training data are a stronger constraint than the choice of the ML method. The most informative inputs generally include precipitation and winds near the balloons' level. However, different models highlight different informative variables, making physical interpretation uncertain. This study also discusses potential limitations, including the intermittent nature of GWMFs and data scarcity, providing insights into the challenges and opportunities for advancing our understanding of these atmospheric phenomena.