In response to the near-threatened status of Handroanthus impetiginosus, primarily due to habitat loss and illegal logging, this study examines how X-ray imaging and cryopreservation impact the seed quality and viability essential for conservation. Seeds initially had a moisture content of 12.3%, reduced to 6.5% through desiccation. X-ray imaging allowed detailed visualization of internal structures, identifying seeds as normal, abnormal, or dead based on damage and development. Normal seeds consistently germinated and produced healthy seedlings, while those with internal damage or excessive desiccation either resulted in abnormal seedlings or did not germinate. Various cryopreservation treatments were tested, including storage at -80°C and liquid nitrogen immersion (LN), with and without vitrification solutions (PSV2; PVS3; PSV2 + 1% phloroglucinol; PSV3 + 1% phloroglucinol). Results indicated that immersion in LN without cryoprotectants achieved the highest germination and seedling viability, whereas vitrification solutions, such as PVS2 and PVS3, negatively affected germination. The study demonstrates that X-ray imaging is an effective tool for assessing seed quality and detecting internal damage, while cryopreservation without cryoprotectants is suitable for long-term seed storage. This work highlights the benefits of combining X-ray assessment with optimized cryopreservation techniques to support conservation of threatened species.