Background: Between March, 2020 and December, 2021 due to cholera and coronavirus disease 2019 (COVID-19) pandemics, there were 1,534 cholera cases with 14 deaths and 136,065 COVID-19 cases with 3,285 deaths reported respectively in Uganda. This study investigated mass vaccination campaigns for the prevention of the two pandemics namely: oral cholera vaccine (OCV) and COVID-19 vaccine coverage; adverse events following immunization (AEFI); barriers and enablers for the vaccine uptake and assessed water, sanitation and hygiene (WASH) conditions in the six cholera and COVID-19 hotspot districts of Uganda. Methods: A household survey was conducted between January and February, 2022 in the six cholera hotspot districts of Uganda which had recently conducted OCV mass vaccination campaigns and had ongoing COVID-19 mass vaccination campaigns. The survey randomly enrolled 900 households with 4,315 persons of whom 2,085 were above 18 years. Data were collected using a data entry application designed in KoBoToolbox and analysed using STATA version 14. Frequencies, percentages, odds ratios, means, confidence intervals and maps were generated and interpreted. Results: The OCV coverage for dose one and two were 85% (95% CI: 84.2—86.4) and 67% (95% CI: 65.6—68.4) respectively. Among the 4,315 OCV recipients, 2% reported mild AEFI, 0.16% reported moderate AEFI and none reported severe AEFI. The COVID-19 vaccination coverage for dose one and two were 69.8% (95% CI: 67.8–71.8) and 18.8% (95% CI: 17.1–20.5) respectively. Approximately, 23% (478/2,085) of COVID-19 vaccine recipient reported AEFI; most 94% were mild, 0.6% were moderate and 2 cases were severe. The commonest reason for missing COVID-19 vaccine was fear of the side effects. For most districts (5/6), sanitation (latrine/toilet) coverage were low at 7.4%—37.4%. Conclusion: There is high OCV coverage but low COVID-19 vaccine and sanitation coverage with high number of moderate cases of AEFI recorded due to COVID-19 vaccines. The low COVID-19 vaccine coverage could indicate vaccine hesitancy for COVID-19 vaccines. Furthermore, incorporation of WASH conditions assessment in the OCV coverage surveys is recommended for similar settings to generate data for better planning. However, more studies are required on COVID-19 vaccine hesitancy.
