Shea butter is becoming increasingly popular in foods, cosmetics and pharmaceutical products. This work aims to study the effect of the refining process on the quality and stability of fractionated and mixed shea butters. Crude shea butter, refined shea stearin, olein and their mixture (1:1 w/w) were analyzed for fatty acids, triacylglycerol composition, peroxide value (PV), free fatty acids (FFA), phenolic (TPC), flavonoid (TFC), unsaponifiable matter (USM), tocopherol and phytosterol content. Additionally, the oxidative stability, radical scavenging activity (RSA), antibacterial and antifungal activities were evaluated. The two main fatty acids in the shea butter samples were stearic and oleic. The refined shea stearin showed lower PV, FFA, USM, TPC, TFC, RSA, tocopherol and sterol content than crude shea butter. A higher EC50 was observed, but antibacterial activity was much lower. The refined olein fraction was characterized by lower PV, FFA and TFC in comparison with crude shea butter, but USM, TPC, RSA, EC50, tocopherol and sterol content was unchanged. The antibacterial activity was higher, but the antifungal activity was lower than those of crude shea butter. When both fractions were mixed, their fatty acid and triacylglycerol composition were similar to those of crude shea butter, but other parameters were different.