The opium poppy (Papaver somniferum) is a strategic crop due to its production of benzylisoquinoline alkaloids (BIAs), valuable pharmaceuticals used for pain relief, cough suppression, and as narcotics. Opium poppy is the sole feasible source for commercial BIA production. Türkiye’s opium poppy cultivars, bred for high BIA content, require yield improvement to maintain global competitiveness. This study employed a proteomic approach to compare protein profiles from various organs of different cultivars with varying BIA content. Three Turkish cultivars were analyzed: TMO T (thebaine), Ofis 2 (morphine), and Ofis NM (noscapine). Protein extracts from specific tissues were examined using LC-MS/MS, and BIA content in dry capsules was quantified via TLC/HPLC analysis. This enabled investigation of connections between protein expression patterns in different organs and cultivars with alkaloid accumulation. Mature capsules exhibited the highest number of significant differentially expressed proteins (DEPs), with Ofis 2 diverging significantly from TMO T and Ofis NM across all tissues in terms of protein expression. Key enzymes in the BIA pathway showed significant upand down-regulation in mature capsules and latex-containing stems. These findings provide insights into differential proteome profiles involved in BIA biosynthetic and regulatory pathways. Future research should focus on unannotated protein functions, multi-omics integration, tissue-specific enzyme localization, and functional gene studies to enhance understanding of BIA biosynthesis. This could facilitate the development of high-yield opium poppy cultivars, ensuring sustainable pharmaceutical production.