Drug-resistant tuberculosis (DR-TB) has become a public health problem throughout the world and about one-third of deaths were attributed to DR-TB from antimicrobial resistance which contributes to 10% of all TB deaths. Sub-Saharan Africa, particularly Ethiopia accounts for a significant number of TB cases. However, the scanty evidence on DR-TB contributing factors could affect the level of this deadly case tackling program. Therefore, this study aimed to assess the factors affecting sputum smear conversion and treatment outcomes among patients with DR-TB in Health facilities in Eastern Ethiopia. A cross-sectional study design was employed from 10 October to 10 November 2021, in the health facilities providing DR-TB services in Harari Region and Dire Dawa city administration. The medical records of 273 DR-TB patients from 10 January 2013 to 27 December 2021, were reviewed using structured checklists. Data were entered into Epidata 3.1 version and exported to STATA 14 version for analysis. The outcome variables were Initial Sputum conversion (converted vs. not-converted) and treatment outcome (Unfavorable vs. Favorable). Sputum examination was performed using both Acid-fast bacillus (AFB) smear microscopy and Löwenstein-Jensen (LJ) culture technique. A binary logistic regression analysis was used to assess the association of independent variables with the first month sputum smear conversion, while a conditional logistic regression model was used to assess the association of treatment outcome with explanatory variables. The associations were reported using adjusted odds ratios (AORs) at a 95% confidence interval. A total of 273 DR-TB patients were included in this study. The unfavorable DR-TB treatment outcome was significantly associated with the history of chewing khat (AOR = 4.38, 95% CI = 1.62, 11.84), having bilateral lung cavity on baseline chest X-ray (AOR = 12.08, 95% CI = 1.80, 2.57), having greater than 2+ smear result at baseline (AOR = 3.79, 95% CI = 1.35, 10.59), and poor adherence (AOR = 2.9, 95% CI = 1.28, 6.82). The sputum smear non-conversion at first month was significantly associated with being Human Immune Virus (HIV)-negative (AOR = 0.37, 0.17, 0.82), having low baseline BMI (AOR = 0.54, 95% CI = 0.29, 0.97), baseline culture > 2++ (AOR = 0.15, 95% CI = 0.05, 0.49) and having greater than 2+ sputum smear result (AOR = 0.09, 95% CI = 0.012, 0.67). Patients with normal chest X-ray at baseline had 3.8 times higher chance of sputum smear conversion on first month (AOR = 3.77, 1.11, 12.77). The overall initial sputum smear conversion and the treatment success rate among DR-TB patients were 52.75 and 66.30%, respectively. The Baseline underweight, HIV-negative, baseline smear > 2+, baseline culture > 2++, and clear lung on baseline X-ray were associated with smear conversion and history of khat chewing, bilateral lung cavity at baseline, having greater than 2+ smear results at baseline, and patients with poor treatment adherence had hostile treatment outcomes. So, strengthening and implementing nutrition assessment and patient counseling during directly observed therapies (DOTs) service and drug compliance could result in early sputum conversion and better treatment outcomes. DR-TB patients with high bacterial load and abnormal lungs on radiologic examination at baseline could need special attention during their course of treatment.