We examined the proteomic profiles of three registered opium poppy cultivars having different alkaloid content. The study was conducted on both stem and capsule organs. A high number of DEPs were identified between the cultivars and the organs. We analyzed DEPs for their contribution in GO terms and KEGG pathways. The up-regulated DEGs were significantly enriched in photosynthesis and translation for morphine-rich and noscapine-rich cultivars, respectively. The data depicted that photosynthesis is crucial for BIA biosynthesis, but different processes are also effective on morphine and noscapine biosynthesis which occur at different branches in the biosynthetic pathway. The protomic profiles revealed that energy demand is more effective in morphine biosynthesis, while translational control has leading role in noscapine biosynthesis. This is the first report demonstrating the organ-based and cultivar-based protein expression differences in mature poppy plant.