The feasibility of the use of two lipid sources and their impact on the cannabinoid profile, terpene fingerprint, and degradation products in medical cannabis oil preparations during 3 months of refrigerated storage time were investigated. LCHRMS-Orbitrap^® and HS-SPME coupled to GC-MS for the investigation of targeted and untargeted cannabinoids, terpenes, and lipid degradation products in Bedrocan^® and Bediol^® macerated oils were used as analytical approaches. As regards the cannabinoid trend during 90 days of storage, there were no differences between PhEur-grade olive oil (OOPH) and medium-chain triglycerides oil (MCT oil) coupled to a good stability of preparations for the first 60 days both in Bedrocan^® and Bediol^® oils. MCT lipid source extracted a significant concentration of terpenes compared to olive oil. Terpenes showed a different scenario since MCT oil displayed the strongest extraction capacity and conservation trend of all compounds during the shelf life. Terpenes remained stable throughout the entire storage period in MCT formulations while a significant decrease after 15 and 30 days in Bediol^® and Bedrocan^® was observed in olive oil. Therefore, MCT oil could be considered a more suitable lipid source compared to olive oil involved in the extraction of medical cannabis for magistral preparations.