Baby carrot is a very perishable product mainly due to the abrasion of the cylindrical carrot root segments. The influence of four different controlled atmospheres (CA) (air, 2 kPa O2 + 15 kPa CO2, 5 kPa O2 + 5 kPa CO2 and 10 kPa O2 + 10 kPa CO2) was studied to maintain quality and prolong the shelf life of baby carrots. Respiration rate (RR), the content of vitamin C, carotenoids and phenolics by HPLC as well as the sensory quality of baby carrots during storage at 4 °C were evaluated. The lowest RR was observed in baby carrots stored under CA containing the lowest O2 concentrations. Baby carrots under low O2 atmospheres preserved the highest vitamin C content, as well as the individual carotenoids. The wound-induced phenolic compounds, mainly trans chlorogenic acid, increased two fold in baby carrots stored under 5 kPa O2 + 5 kPa CO2. In general, CA maintained the overall visual quality of baby carrots up to 8 days. Controlled atmosphere of 5 kPa O2 + 5 kPa CO2 can be recommended as an optimum atmosphere to maintain quality of baby carrots, increasing bioactive compounds such as chlorogenic acid and avoiding anaerobic fermentation in case of temperature abuse.