Although numerous studies have examined the effects of climate variability on armed conflict, the complexity of these linkages requires deeper understanding to assess the causes and effects. Here, we assembled an extensive database of armed conflict, climate, and non-climate data for South Asia. We used structural equation modeling to quantify both the direct and indirect impacts of climate variability on armed conflict. We found that precipitation impacts armed conflict via direct and indirect effects which are contradictory in sign. Temperature affects armed conflict only through a direct path, while indirect effects were insignificant. Yet, an in-depth analysis of indirect effects showed that the net impact is weak due to two strong contradictory effects offsetting each other. Our findings illustrate the complex link between climate variability and armed conflict, highlighting the importance of a detailed analysis of South Asia's underlying mechanisms at the regional scale.