By using a geo-coded disaggregated dataset in sub-Saharan Africa over the period 1997–2013, we exploit year-to-year rainfall variation as an instrumental variable to estimate the causal effect of economic shocks on civil conflict conditional on governance quality. We confirm earlier findings that adverse rainfall shocks increase the likelihood of conflict in sub-Saharan Africa. We also investigate the role of governance quality on conflict in sub-Saharan Africa. The results underscore that improvement of governance quality can effectively mitigate the detrimental effect of negative income shocks on regional peace. However, due to the limited penetration of countrywide governance structures, this effect of governance quality is more significant in areas closer from the capital cities than in the remote areas.