Only little is known about the true extent of COVID-19 in Somalia. The study aims to assess the seroprevalence of the COVID-19 pandemics in the Benadir region using SARS-CoV-2 antibodies and estimate the number of inhabitants infected with SARS-CoV-2. Population-based cross-sectional survey was conducted to measure the seroprevalence of antibodies against SARS-CoV-2 in the Benadir region (Mogadishu city). In the study, we enrolled 2500 Mogadishu city residents aged ≥18 years who did not receive the SARS-CoV-2 vaccine. The overall seroprevalence of IgG/IgM anti-SARS-CoV-2 antibodies was 44.8%. The seropositivity in females (56.6%) was higher than in males (46.2%). The trend in seropositivity increased with age; however, the variation was only significant in the age group 38–57 with an odds ratio and p-value of 4.11 (1.475–11.47), p = 0.007. Families with >5 members (47.2%) were more likely to test positive than those with <5 members (37%). Participants who reported COVID-19 symptoms during the pandemics or who had contact with COVID-19 patients had significantly increased IgG prevalence. Participants with larger families, individuals working in the public sector, and students showed significant seropositive results. Therefore, precautionary measures should be heightened for individuals working in the public sector.