Lilies are important crops that are commonly used as cut flowers (Lilium spp.) and edible bulb crops (Lilium davidii var. unicolor). However, virus infections can significantly impact the quantity and quality of lily production. Various methods have been developed to eliminate viruses in lilies, including in vitro culture and virus detection techniques. Meristem culture is the most effective method, which can be combined with other techniques such as thermotherapy and chemotherapy. Nonetheless, virus elimination is affected by several factors, including cultivar, explants used, virus type, and duration of treatments. Efficient diagnostic methods, such as serological and molecular techniques, have been developed to detect viral infections in lilies, including enzyme-linked immunosorbent assay (ELISA) and real-time reverse transcriptase polymerase chain reaction (real-time RT-PCR). However, cross-contamination and multiple-virus contamination can lead to unreliable results, and more sophisticated protocols and systems have been developed to address these issues. The objective of this review is to provide a comprehensive overview of the development of lily virus eradication, detection strategies, challenges, and solutions associated with these procedures, and how more sophisticated approaches such as multiplex RT-PCR, indirect ELISA (ID-ELISA), immunocapture RT-PCR (IC-RT-PCR), and immunochromatographic test strips (ICSs) can alleviate some of these setbacks.