Background Biomedical waste management is an important precondition to safeguard the healthcare workers and community members, as well as the environment, from being contaminated with infectious substances. However, biomedical waste management practices during the pandemic era of COVID-19 were unknown. Objective This study was aimed to assess biomedical waste management practices and associated factors among health care workers during the COVID-19 pandemic era at metropolitan city private hospitals, Amhara Region, Ethiopia. Methods An institutional-based cross-sectional study was conducted at metropolitan city private hospitals in Amhara Region. Simple random sampling was used to select 431 study participants. Data were collected through a self-administered questionnaire and observational checklists. The data were cleaned, coded, and entered into the Epi-data version 4.6, and then exported to SPSS version 20. for analysis. Variables with a p-value less than 0.05 were considered as significant factors in multivariable logistic regression analysis and AOR with a 95% confidence level was used to measure the strength of association. Results The proportion of health care workers who had good practices in biomedical waste management was 49.4%. Participants who had MSc education level, [AOR = 4.20, 95% CI (1.01, 17.40)], Bachelor degree [AOR = 3.52, 95% CI (2.13, 5.82)], got training on biomedical waste management [AOR = 4.33, 95% CI (2.71, 6.93)], access to color-coded three bins in their working department [AOR = 6.24.95% CI (3.84, 10.13)] and those who had good attitude (AOR = 2.64, 95% CI (1.65, 4.22), were significantly associated with biomedical waste management practices in private hospitals. Conclusion The practice of biomedical waste management in the study area was low. Level of education, taking training on biomedical waste management, availability of color-coded three bins, and attitude of health care workers were significantly associated with biomedical waste management practices. Hence, in-service training is recommended to improve biomedical waste management practices.