This study investigates the factors associated with the self-reported ability to comply with home isolation after a COVID-19 diagnosis in vulnerable communities in Salvador (Bahia) and Rio de Janeiro (Brazil). It is a cross-sectional study including 324 participants from the project “Expansion of testing, quarantine, e-health, and telemonitoring strategies to address the COVID-19 pandemic in Brazil” (TQT COVID-19). Results indicate that high household density (≥0.5 persons per room) was significantly associated with a lower ability to isolate (adjusted OR=0.41; 95% CI: 0.20–0.82; p=0.01). Housing conditions, more than individual characteristics, were decisive for adherence to home isolation. Findings highlight the need for public policies that address structural inequalities and expand access to adequate housing in vulnerable settings.