A carotenoid-rich extract from Lycium barbarum L. was added to extra virgin olive oil (EVOO), obtaining a carotenoid-enriched oil (EVOOCar). The oxidative stability of EVOO and EVOOCar was evaluated during long-term storage of 28 weeks at room temperature, by measuring some classical parameters (acidity and peroxide values, spectrophotometric coefficients, fatty acid composition) and the content of minor compounds (i.e., α-tocopherol and lutein). At the end of the storage, higher content (p < 0.01) of α-tocopherol in EVOOCar in respect to EVOO were observed. Zeaxanthin dipalmitate, the most abundant carotenoid compound of Goji berries, decreased slightly (p < 0.05) in EVOOCar until the end of the storage. In regard to polyphenols, an ultra-high-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UHPLC/QTOF-MS) using untargeted metabolomics was carried out. This latter approach discriminated the two oil samples during long-term storage, allowing to identify also the phenolic classes most exposed to significant variations during storage (i.e., mainly lignans and flavones). Besides, the addition of Goji carotenoids preserved the stability of tyrosol equivalents in EVOOCar during long-term storage. These results highlighted that the enrichment of EVOO with a carotenoid-rich extract can improve the shelf-life and nutritional value of added-oil, protecting EVOO natural antioxidants during long-term storage.