Oleosomes are the main energy source in plant seeds and play a crucial role in the early phase of germination. However, the structural and biochemical changes oleosomes undergo during native seedling development remain elusive. Using label-free coherent Raman microscopy, we show the highly dynamic reorganization of oleosomes in soybean seeds in situ duing the first eight days of germination. Initially homogenously distributed over the entire cotyledon, these lipid reservoirs are depleted from the outer cell layers and undergo two cycles of growths and shrinkage. These cycles coincide with augmented activities of proteases, phospholipases and an increase of lipolysis, respectively. At the same time, oleosins, the main oleosome coating protein, disappear gradually during germination. Our results show that oleosomes are actively remodeled during germination and may serve as a vertex connecting seedling development, energy utilization, and enzymatic activity.