In winter oilseed rape (Brassica napus L.), vernalization, prolonged cold exposure, is essential for spring flowering. Although transcriptomic changes in leaves during vernalization are studied, the taproot, a key storage organ, remains unexplored. Recently, high nitrogen (N) and carbon (C) compound levels were observed in the taproot post-vernalization, suggesting potential metabolic activities in this organ during this period. To decipher this, an integrative study combining morphological, ionomic, proteomic, and targeted biochemical analysis was conducted. This study revealed that the taproot is the only compartment that shows net gain in biomass during vernalization and confirmed its role in storing C and N reserves. A comparative proteomic analysis between the beginning and the end of the vernalization period showed that this storage is the result of a strong modulation of proteins involved in N and C metabolisms. Additionally, the up-accumulation of proteins involved in the starch and amino acid metabolisms is consistent with the increase in the starch and amino acid amounts in the taproot during vernalization. Amino acids from the glutamine family are especially accumulated, with proline being the most over-accumulated (127-fold), highlighting the initiation of a protective metabolism in the taproot during the cold stress period related to vernalization. This study also reveals the storage of macro- and microelements, notably iron, copper, and zinc. These findings provide a deeper understanding of the development and maintenance of specific metabolic activities in the taproot of B. napus during vernalization, ensuring the accumulation of essential N and C reserves for subsequent growth and development.