Objective This study aims to assess the magnitude and associated factors of poor medication adherence among diabetic and hypertensive patients visiting public health facilities in Addis Ababa, Ethiopia during the COVID-19 pandemic. Methods A multi-site cross-sectional design was conducted from 1.sup.st through 30.sup.th of August 2020 at public health facilities of the study area. Adult outpatients with T2DM and hypertension visiting hospitals and health centers were included in the study. A proportion to size allocation method was used to determine the required sample size per facility. Data was collected using the 8-item Morisky medication adherence scale. Descriptive statistics and binary logistic regression were used to analyze data. A 95% confidence interval and p[less than or equal to]0.05 statistical significance was considered to determine factors associated with poor medication adherence. Results A total of 409 patients were included in the present study. About 57% of the patients reported that the COVID-19 pandemic has posed negative impacts on either of their follow-up visits, availability of medications, or affordability of prices. And, 21% have reported that they have been affected in all aspects. The overall magnitude of poor medication adherence was 72%. Patients with extreme poverty were more likely to have good medication adherence (AOR: 0.59; 95%C.I: 0.36-0.97), whereas attendance to a health center (AOR: 1.71; 95%C.I: 1.02-2.85), presence of comorbidity (AOR: 2.05; 95%C.I: 1.13-3.71), and current substance use history (AOR: 11.57; 95%C.I: 1.52-88.05) predicted high odds of poor adherence. Conclusion Over a three-fourth of the patients, in the study setting, have poor adherence to their anti-diabetic and antihypertensive medications. Health facility type, income level, comorbidity, and current substance use history showed a statistically significant association with poor adherence to medication. Stakeholders should set alternative strategies as perceived impacts of the COVID-19 pandemic on medication adherence are high in the study area.