The transition metals (Fe, Zn, Cu, and Mn) which are also considered as the micronutrient are essential for plants as they regulate various cellular metabolic activities that promote proper plant growth and development. These transition metals are also involved in photosynthesis, respiration, chlorophyll synthesis, transcription, translation, cell division, and cell elongation. However, their deficiencies and toxicity may hamper the plant growth and metabolism. Therefore, to avoid their toxicity, storage and distribution of metals in several cellular compartments are highly regulated for proper plant metabolism and growth. Alteration in metal composition of cellular organelles impairs many crucial metabolic processes of plant and further affects plant growth and yield trait. Therefore, transition metal homeostasis and cellular compartmentalization are the important processes for proper plant metabolism. This chapter highlights the transition metal homeostasis in several organelles like chloroplast, mitochondria, vacuole, vesicles, and Golgi bodies, and also covers the involvement of transporters and proteins in compartmentalization and maintaining homeostasis for proper developed biofortified crop. This chapter also includes the role of transition metals (Fe, Zn, Cu, and Mn) in plant growth and development which will help us to assess their role for sustainable agriculture and crop improvement.