Trust in institutions is a key driver to shape population attitudes and behavior, such as compliance of non-pharmaceutical interventions (NPI). During the COVID-19 pandemic, this was fundamental and its compliance was supported by governmental and non-governmental institutions. Nevertheless, the situation of political polarization in some countries with decentralized health systems increased the difficulty of such interventions. This study analyzes the association between non-pharmaceutical interventions’ compliance and individual perception regarding institutions’ performance during the COVID-19 pandemic in Brazil. A web survey was conducted in Brazil between November 2020 and February 2021. Bivariate analysis and ordered logit regressions were performed to assess the association between NPIs compliance and perceived institutions’ performance. Results suggest a negative association between NPIs’ compliance and Federal Government and Ministry of health perceived performance, which may reflect the political positioning of the respondents. Moreover, we find a positive association between NPI compliance and the perceived performance of the remaining institutions (state government, federal supreme court, national congress, WHO, media and SUS). Our contribution goes beyond the study of a relationship between non-pharmaceutical interventions’ compliance and institutions’ performance, by pointing out the importance of subnational and local governmental spheres in a decentralized health system, as well as highlighting the importance of social communication based on health organizations’ information and scientific institutions.