The feeling of loneliness is a major public health concern associated with multiple somatic and psychiatric illnesses. Studies have shown increasing incidence of loneliness in the general population during the first wave of the COVID-19 pandemic. Homeless individuals are a particularly vulnerable group; however, little is known about loneliness among homeless individuals. We therefore aimed to examine the prevalence of loneliness among homeless individuals during the pandemic. Furthermore, we estimated the association between loneliness and sociodemographic and lifestyle factors, as well as the self-perceived risk of contracting COVID-19. Data from the Hamburg survey of homeless individuals were used, including 151 homeless individuals that were recruited in spring of 2020. Loneliness was measured by the 3- item version of the UCLA-3 Loneliness Scale. To summarize, 48.5% of the participants experienced loneliness. Multiple linear regressions showed increased loneliness to be associated with male gender (β = 1.07, p = 0.01), being single (β = 1.33, p = 0.00), originating from Germany (β = 1.48, p = 0.00), high frequency of sharing a sleeping space with more than three people (β = 0.42, p = 0.02) and a higher self-perceived risk of contracting COVID-19 (β = 0.41, p = 0.02). On the contrary, there was no association of loneliness with age, educational level, chronic alcohol consumption or frequently sharing a sleeping space. In conclusion, the magnitude of loneliness among homeless individuals during the pandemic was highlighted. Description of factors determining loneliness may help to identify homeless individuals at risk.