Background: Individuals experiencing homelessness residing in congregate homeless have increased risk for SARS-CoV-2 infection. Prevalence of asymptomatic SARS-CoV-2 in congregate shelters is high, but shelter characteristics associated with SARS-CoV-2 transmission are currently unknown. Methods: We conducted a cross-sectional, multicenter cohort study across five congregate shelters in Rhode Island. We tested people 18 years of age and older staying in Rhode Island congregate shelters in April 2020 during the COVID-19 pandemic. A survey instrument was designed and implemented based on an a priori sample size. All consented participants reported basic demographics, recent travel, duration of time at the shelter, any symptomatology, and had their temperature and pulse oximetry measured. Each participant was tested for COVID-19 using nasopharyngeal swabbing. Shelter characteristics about location, occupancy, resident length of stay, and COVID-19 mitigation strategies were collected through structured phone questionnaire with shelter staff. Results: A total of 302 individuals were screened and 299 participated across five homeless shelters. The median age was 47.9 (range 18-85) and 20% were female. Of the 299 participants, 35 (11.7%) were positive for SARS-CoV-2; rates varied among shelters, ranging from 0% to 35%. Among the participants in the study, 5% had a new cough, 4% shortness of breath, and 3% reported loss of taste or smell. Symptom prevalence did not vary significantly between positive and negative SARS-CoV-2 groups. Regular symptom screening was not associated with lower infection rates. Shelters with higher rates of positivity were in more densely populated areas, cared for a more transient populations, and instituted fewer social distancing practices for sleeping arrangements or mealtimes. Conclusions and Relevance: Residents of congregate shelters are at increased risk for asymptomatic transmission of SARS-CoV-2. To reduce transmission and enable continuation of low-threshold shelter services, there is a need for universal testing, implementation of infection control and physical distancing measures within congregate shelters, and expansion of non-congregate supportive housing.