Background: Substantial progress has been made in reducing the burden of malaria in Africa since 2000, but those gains could be jeopardised if the COVID-19 pandemic affects the availability of key malaria control interventions. The aim of this study was to evaluate plausible effects on malaria incidence and mortality under different levels of disruption to malaria control. Methods: Using an established set of spatiotemporal Bayesian geostatistical models, we generated geospatial estimates across malaria-endemic African countries of the clinical case incidence and mortality of malaria, incorporating an updated database of parasite rate surveys, insecticide-treated net (ITN) coverage, and effective treatment rates. We established a baseline estimate for the anticipated malaria burden in Africa in the absence of COVID-19-related disruptions, and repeated the analysis for nine hypothetical scenarios in which effective treatment with an antimalarial drug and distribution of ITNs (both through routine channels and mass campaigns) were reduced to varying extents. Findings: We estimated 215·2 (95% uncertainty interval 143·7–311·6) million cases and 386·4 (307·8–497·8) thousand deaths across malaria-endemic African countries in 2020 in our baseline scenario of undisrupted intervention coverage. With greater reductions in access to effective antimalarial drug treatment, our model predicted increasing numbers of cases and deaths: 224·1 (148·7–326·8) million cases and 487·9 (385·3–634·6) thousand deaths with a 25% reduction in antimalarial drug coverage; 233·1 (153·7–342·5) million cases and 597·4 (468·0–784·4) thousand deaths with a 50% reduction; and 242·3 (158·7–358·8) million cases and 715·2 (556·4–947·9) thousand deaths with a 75% reduction. Halting planned 2020 ITN mass distribution campaigns and reducing routine ITN distributions by 25%–75% also increased malaria burden to a total of 230·5 (151·6–343·3) million cases and 411·7 (322·8–545·5) thousand deaths with a 25% reduction; 232·8 (152·3–345·9) million cases and 415·5 (324·3–549·4) thousand deaths with a 50% reduction; and 234·0 (152·9–348·4) million cases and 417·6 (325·5–553·1) thousand deaths with a 75% reduction. When ITN coverage and antimalarial drug coverage were synchronously reduced, malaria burden increased to 240·5 (156·5–358·2) million cases and 520·9 (404·1–691·9) thousand deaths with a 25% reduction; 251·0 (162·2–377·0) million cases and 640·2 (492·0–856·7) thousand deaths with a 50% reduction; and 261·6 (167·7–396·8) million cases and 768·6 (586·1–1038·7) thousand deaths with a 75% reduction. Interpretation: Under pessimistic scenarios, COVID-19-related disruption to malaria control in Africa could almost double malaria mortality in 2020, and potentially lead to even greater increases in subsequent years. To avoid a reversal of two decades of progress against malaria, averting this public health disaster must remain an integrated priority alongside the response to COVID-19. Funding: Bill and Melinda Gates Foundation; Channel 7 Telethon Trust, Western Australia.