BACKGROUND: While the impact of the COVID-19 pandemic has been well documented in high-income countries, less is known about the health effects in Somalia, where health systems are weak and vital registration is underdeveloped. METHODS: We used remote sensing and geospatial analysis to quantify burial numbers from January 2017 to September 2020 in Mogadishu. We imputed missing grave counts using surface area data. Simple interpolation and a generalised additive mixed growth model were used to predict actual and counterfactual burial rates by cemetery and across Mogadishu during the most likely period of COVID-19 excess mortality and to compute excess burials. We undertook a qualitative survey of key informants to determine the drivers of COVID-19 excess mortality. RESULTS: Burial rates increased during the pandemic, averaging 1.5-fold and peaking at a 2.2-fold increase on pre-pandemic levels. When scaled to plausible range of baseline crude death rates, the excess death toll between January and September 2020 was 3200-11 800. Compared with Barakaat Cemetery Committee's burial records, our estimates were lower. CONCLUSIONS: Our study indicates considerable underestimation of the health effects of COVID-19 in Banadir and an overburdened public health system struggling to deal with the increasing severity of the epidemic in 2020.