Wine lees, a winemaking by-product, have high potential for reuse due to their significant phenolic content and antioxidant capacity. To preserve their composition and enhance their feasibility for incorporation into food products, this study evaluated the effects of oven drying (40 °C) and freeze-drying on the physicochemical and nutritional characteristics of malolactic lees, as well as the impact of the storage time. Samples were analyzed at 0, 45, and 90 days of storage at 25 °C under light exposure conditions. Total phenolic content was determined by Folin–Ciocalteu, antioxidant activity by DPPH and FRAP assays, and phenolic groups by HPLC-DAD-FD. Both methods preserved a high protein content (~20%), with 44.66% essential amino acids and an essential amino acid index of 1.55, indicating high-quality proteins. The freeze-dried lees showed a higher phenolic content (77.92 mg GAE/g), whereas the oven-dried lees exhibited greater antioxidant activity, likely due to the formation or release of bound phenolic compounds induced by thermal processing. Among the phenolic groups, tannins were the most favored in terms of preservation. Storage time significantly influenced the parameters evaluated, indicating the impact of drying on stability. While freeze-drying better preserved phenolic compounds, oven drying was considered the most suitable option for large-scale application.