Leaves of Scorzonera incisa DC. (Asteraceae) are eaten raw against diabetes and headache. Evaluation of medicinal, edible plants using profiling methods has become a common phenomenon. Petroleum ether (PE), ethyl acetate (EA), and n-butanol (BU) fractions were prepared from ethanol extract of the aerial parts of the plant. Isolation by HPLC and phenolic profiling by validated LC-MS/MS method with 53 compounds were conducted on the EA fraction. GC-MS method was used to profile the PE fraction. In-vitro inhibitory activities of all fractions against α-amylase, α-glucosidase, AChE, BChE, tyrosinase and urease enzymes were measured. Isoorientin, vitexin, cynaroside and chlorogenic acid were isolated and characterized from the EA fraction as major compounds. LC-MS/MS analysis quantified 36 compounds in the EA fraction. 20 compounds were tentatively determined in the PE fraction. Compounds with the same molecular and fragment ions, a low percentage of identified compounds, and very close polarities were revealed to be some limits of the nature for LC-MS/MS profiling. Particularly, the presence and amount of substances other than the standard compounds used in the profiling methods and possible misdetections should not be neglected in evaluating medicinal plants and establishing a correlation between compounds and bioactivity.