Peeling may result in changes in carrot’s nutritional properties; therefore, the present study focused on its effect on the retention of principal nutrients (minerals, sugars, organic acids) and antioxidants (carotenoids and phenols) in the peeled roots of two landraces (‘Carota a punta lunga’—CPL and ‘Carota a punta tonda’—CPT) and a hybrid cultivar (‘Presto’) grown in the area of the “Salterns of Margherita di Savoia” area (Puglia region). The peel had a higher concentration of cations (+92%), organic acids (+103%), carotenoids (+42%), and phenolic acids (seven times) than root flesh. For each chemical class, the most abundant components were K, malic acid, ß-carotene, and chlorogenic acid, respectively. The two landraces stand out for the accumulation of the phenolic acids and ß-carotene, whereas the peel of ‘Presto’ was distinguished by the concentration of Ca and ascorbic and pyruvic acids. The root flesh had a greater accumulation of simple sugars, nitrate (mainly in CPL), oxalic acid, and in particular in the flesh of ‘Presto’, of Na and Cl. For local varieties, peel removal seems to impact the nutritional and antioxidative properties of carrots more consistently compared to the advanced cultivar, since it represents on average 21% and 59% of the total carotenoids and phenols, respectively, of the intact roots.