Tuberculosis is a communicable disease caused by Mycobacterium tuberculosis (M. tuberculosis). It is the leading cause of death ranking above HIV/AIDS. Most of the healthcare facilities in Ethiopia still use Ziehl Neelsen (ZN) microscopy to diagnose pulmonary tuberculosis (PTB) rather than GeneXpert. However, an agreement between the two methods, the prevalence of rifampicin resistance and risk factors associated with M. tuberculosis among PTB suspected patients at Durbete Primary Hospital (DPH) were not known and reported previously. Therefore, this study aimed to compare ZN microscopy and geneXpert in the diagnosis of PTB and to determine rifampicin resistance and associated risk factors among suspected patients at DPH. A hospital-based cross-sectional study was conducted among 180 PTB suspected patients at DPH from February to June 2022. Sputum was examined both by ZN microscopy and geneXpert. Data were entered into an excel sheet and exported to SPSS version 26 for analysis. The prevalence of PTB was calculated with its 95% CI. Binary logistic regression was done to determine the strength of association between dependent variables and possible risk factors. Variables with a p value of less than 0.25 during univariate logistic regression analysis were selected for multivariate analysis. A p-value of less than 0.05 was used to indicate statistical significance. Cohen’s Kappa was used to measure the levels of agreement between both diagnosis methods. Of the total 180, PTB suspected patients who participated in the study, 16 (8.89%) and 13 (7.22%) of them were identified as having PTB by Xpert assay and ZN microscopy respectively. One (6.25%; 1/16) Xpert positive specimen was resistant to rifampicin. The overall prevalence of PTB was 17 (9.44%). Participants who had an unknown history of hypertension (AOR = 8.483; 95% CI 1.059-67.935) and contact with known PTB cases (AOR = 16.108; 95% CI 1.983-130.844) were significantly associated with the prevalence of PTB (p<0.05). The Cohen’s Kappa agreement between the two diagnosis methods was good (K = 0.80). This study showed a high prevalence of PTB among suspected patients. This study also showed a good agreement between ZN microscopy and Xpert assay in the diagnosis of PTB. Periodic surveillance of PTB and educating the local community about the disease and major risk factors such as contact with known PTB cases identified in the present study are necessary to reduce the prevalence of PTB.