Background The study sought to determine factors associated with prolonged smear positivity in multidrug-resistant tuberculosis (MDR-TB) patients following an appropriate management.Methods Newly diagnosed patients [(100 MDR-TB and 100 drug-susceptible TB (DS-TB)] were enrolled between June 2017 and May 2018. Clinical and radiological findings were recorded. Sputum samples were collected for Xpert® MTB/RIF and line probe assays (LiPA). Microscopic tests, including smear grading, were performed at baseline, 4, 8 and 12 weeks post anti-TB therapy. Kaplan-Meier and Cox regression analyses were performed using SPSS v23 with ρ set at ≤ 0.05. Results Of the 200 patients (median age of 34.8 years), 114 (57%) were HIV positive. After 12 weeks of treatment, there was a significant microscopy conversion rate among DS-TB patients [43/45 (95.6%)] as compared to MDR-TB patients [54/69 (78.3%)] (ρ = 0.009), all co-infected with HIV. Similarly, among HIV negative patients, a significant microscopy conversion rate was noted among DS-TB patients [48/55(69.6%)] as compared to MDR-TB patients [21/31(30.4%)] (ρ = 0.03). Time to microscopy conversion was 4.58 ± 2.97 weeks and 5.69 ± 3.25 weeks for HIV positive patients aged ≥35 years and <35 years, respectively whilst among HIV negative patients, time to conversion was5.00 ± 2.83 weeks and 6.86± 3.59 weeks for those aged ≥35 years and <35 years, respectively (ρ = 0.003). There was a significant association between CD4+ T cell counts at initiation of TB treatment and smear microscopy conversion rates after 12 weeks (ρ = 0.010). At 8 weeks of anti-TB therapy, all MDR-TB patients whose baseline smear microscopy score ranged from scanty to 1+ converted negative whilst 25% of patients with score ≥2+ at baseline remained positive at the end of 12 weeks of treatment (ρ = 0.014). Multivariate Cox regression showed that only baseline smear microscopy grade was independently associated with prolonged smear positivity in MDR-TB patients at 12 weeks (ρ = 0.014).Conclusion Baseline microscopy score ≥2+ is key determinant for prolonged MDR-TB smear positivity beyond 12 weeks of anti-TB therapy. This indicator, though less sensitive than culture, can be used in poor resource settings.