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Why did some Bolivian departments have more success containing COVID-19 than others? We argue that low government legitimacy hampers coordinated responses to national crises, particularly where political polarization is severe and the crisis response becomes politicized. Low legitimacy can intensify the challenges of poverty and poor infrastructure. An original dataset of daily observations on subnational coronavirus policy and cell phone mobility data, paired with administrative data on cases and deaths, suggests that political divisions influenced governors’ policy implementation and citizens’ compliance. In departments that opposed the president, policies were more likely to deviate from the stricter national policy while mobility and protest activity were high. In departments aligned with the president, local policy followed national policy and citizens complied with policy and quarantine restrictions for a longer period of time.