This study aims to assess the magnitude and associated factors of poor medication adherence among patients with diabetes and hypertension visiting health facilities in Addis Ababa, Ethiopia, during the COVID-19 pandemic. A total of 409 patients were included in the study. Some 57% patients reported that the COVID-19 pandemic had a negative impact on their follow-up visits, availability of medicines or affordability. And 21% reported being affected in all aspects. The overall magnitude of poor medication adherence was 72%. More than three-quarters of patients participating in the study had poor adherence to diabetes and hypotensive medication. Type of healthcare facility, income level, comorbidities and history of substance use showed a statistically significant association with poor medication adherence. Stakeholders should identify alternative strategies, as the perceived impact of the COVID-19 pandemic on medication adherence is high in the study area.