The Himalayan flora is renowned for its rich biodiversity, endemism, and ecological importance, making it a precious natural resource. Within this flora, the Fritillaria genus, belonging to the Liliaceae family, comprises endangered medicinal species distributed widely in temperate zones in the north hemisphere. Esteemed for their notable therapeutic attributes, these plants possess an abundance of bioactive compounds, which account for their valuable medicinal properties. Different parts of the Fritillaria plant, such as bulbs, are employed in herbal medicine due to their anti-cough, mucus-expelling, and anti-asthma properties. Notable isosteroidal alkaloids found in Fritillaria spp. include sipeimine, peimine, and peiminine, while major steroidal alkaloids include puqiedinone and peimisine. This review comprehensively summarizes the diverse biotechnological interventions and advancements employed for in vitro establishment and the enhancement of specialized metabolite production in Fritillaria species. In the realm of in vitro propagation, both direct and indirect pathways are followed, utilizing various explants. Detailed discussions are provided on the optimized tissue culture propagation methods employing explants such as bulb scales, seeds, leaves, shoots, protoplasts, etc. A deeper understanding of secondary metabolites and their metabolic pathways is essential for investigating metabolite upscaling, and thus, the application of omics sciences, including genomics, transcriptomics, and metabolomics, is thoroughly reviewed. By utilizing omics technologies, researchers can successfully upscale metabolite production and gain valuable insights into the biosynthesis and regulation of the bioactive compounds present in Fritillaria. These advanced methodologies offer promising prospects for enhancing our understanding of Fritillaria species and maximizing the production of valuable bioactive compounds for medicinal applications.