Objective To assess the antioxidant and anti-inflammatory activities as well as to determine the flavonoids and phenolic acids content of active fractions. Methods Two medicinal plant samples were extracted successively in Soxhlet apparatus with n-hexane, dichloromethane, acetonitrile, ethyl acetate, methanol and n-butanol. Five methods were used to evaluate the antioxidant activity. Anti-inflammatory activity was done through the inhibition of the cyclooxygenase enzymes (COX-1 and COX-2). Polyphenolic compounds were analyzed by using a spectrophotometrical and high performance liquid chromatography-mass spectrometry (HPLC-MS) methods. Results The data showed that the stem leaves extracts of Commiphora africana and Loeseneriella africana possessed significant in vitro antioxidant and anti-inflammatory activities. Polar extracts had radical scavenging effects and they reduced iron (III). The prostaglandin production was significantly stopped by acetonitrile and methanol extracts. These biological activities were supported by some bioactive compounds quantified by using the HPLC-MS. p-Coumaric acid, ferulic acid, isoquercitrin, quercitrin, quercetin, rutin, kaempferol and apigenin were the most metabolites quantified. Conclusions The present study may explain the effectiveness of plants in traditional medicine of Burkina Faso, singularly Commiphora africana and Loeseneriella africana. The next investigation was to sub-fractionate the methanol fraction in order to isolate new antioxidant and/or anti-inflammatory compounds.