Anthropogenic activity drives extensive tropical deforestation, particularly in Southeast Asia where 16% of total forest cover was lost between 2000 and 2020. While land surface changes significantly affect the atmosphere, their net impact on convective clouds is not well-constrained. Here, we use satellite data to provide the first observational evidence that long-term deforestation in Southeast Asia robustly alters cloud properties, and that the magnitude of this response depends on the atmospheric environment. Deforestation drives a shift towards more widespread, shallower clouds during the daytime, with amplified effects in dry inland areas compared with moist coastal regions. Aerosols only weakly modulate the cloud fraction response, but offset the cloud top height response to deforestation, suggesting the influence of aerosol indirect effects. We conclude that the local signature of forest loss is not uniform, and regional differences in climatology must be considered when assessing deforestation impacts on clouds and the climate system.