Poor management of waste can cause serious disease to healthcare personnel, cleaners, waste handlers, patients and the public. An observation-supported cross-sectional study was conducted to assess healthcare waste (HCW) management practice and professional, management and resource availability-associated factors among healthcare workers of 23 public health facilities in Southwest Shewa Zone, Oromia regional state, Ethiopia, 2021. A total of 424 health workers participated in this study. The level of proper healthcare waste management (HCWM) practice was 38.4%. Lack of knowledge on different methods of healthcare waste treatment (adjusted odds ratio (AOR): 0.101, 95% confidence interval (CI) (0.042, 0.242, p < 0.05)), lack of knowledge about the types of healthcare waste (AOR: 0.136, 95% CI (0.039, 0.481, p < 0.05)), lack of knowledge on the use of different colour-coded waste bin and safety box (AOR: 0.145, 95% CI (0.040, 0.520, p < 0.05)), and healthcare workers who had no training/orientation on HCWM practice (AOR: 0.396, 95% CI (0.245, 0.639, p < 0.05)) were less likely to practice effective HCWM compared to their counterparts. The current HCWM practices in studied health facilities was inadequate. Professional knowledge and availability of training were independently associated with HCWM practice. Therefore, regular orientation during employment and on-job training on HCWM practice, regular monitoring and supervision of HCWM are important. Further research should be conducted on the area of HCWM, and its associated environmental impacts by using more strong methods and wider health facilities.