Background: Extrapulmonary tuberculosis (EPTB) poses a diagnostic challenge due to its paucibacillary nature and low diagnostic yield of traditional methods. Molecular diagnostic tools like Xpert MTB/RIF, Xpert MTB/RIF Ultra, and Truenat MTB offer promising alternatives for the rapid and higher detection rates for pulmonary TB samples. However, the yield of these newly introduced molecular tests on extra-pulmonary samples requires country-specific evaluation and comparative analysis. Methodology: This study evaluated the diagnostic performance of Xpert MTB/RIF, Xpert MTB/RIF Ultra, and Truenat MTB assays in detecting EPTB on 211 clinical specimens collected at a tertiary care centre of central India. The assays� sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPP) were compared against a composite reference standard. Results: Xpert MTB/RIF Ultra exhibited the highest sensitivity (50) for EPTB detection, outperforming the standard GeneXpert MTB/RIF (29.4) and Truenat MTB (35.3), with comparable specificity across all three assays. Among the specimen types, pus samples demonstrated the highest (value) diagnostic yield. These findings highlight the superior diagnostic capabilities of Xpert MTB/RIF Ultra, particularly in paucibacillary cases. Conclusion: Xpert Ultra demonstrates superior sensitivity for EPTB detection compared to Xpert MTB/RIF and Truenat MTB, making it a promising tool to enhance diagnostic accuracy in paucibacillary TB. Its adoption as a standard diagnostic method could significantly improve EPTB management. These findings advocate for integrating advanced molecular diagnostics into routine tuberculosis workflows to reduce diagnostic delays and improve patient outcomes. Clinical trail number: Not applicable. © 2025 Elsevier B.V., All rights reserved.