Black carrot ( ssp. var. Alef.) is widely recognized for its bioactive compounds and antioxidant properties. The black carrot of Cuevas Bajas (Málaga) is a local variety characterized by a black/purple core, which differs from other black carrot varieties. Therefore, this autochthonous variety was characterized according to the root size and the harvesting season by means of a study of its antioxidant capacity analyzed by three methods, its total carotenoids content, and its sugars and phenolic compounds profile by ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-MS). A total of 20 polyphenolic compounds were quantified in 144 samples analyzed. The anthocyanidins group was observed to be the most abundant, followed by the hydroxycinnamic acids group. Moreover, pelargonidin 3-sambubioside was observed in black carrot for the first time. The medium-sized carrots presented the highest content of phenolic compounds, largely due to their significantly higher anthocyanidins content. Comparatively, the small carrots showed a higher content of simple sugars than the large ones. Regarding the influence of season, significantly higher quantities of glucose and fructose were observed in the late-season carrots, while sucrose was the main sugar in early-season samples. No significant differences were observed in the total carotenoid content of black carrot.