Industrial application of icariin and baohuoside I has been hindered by the short supply to a great extent. In this work, a novel GH78α-l-rhamnosidase AmRha catalyzed the bioconversion of low-value epimedin C in crudeEpimedium Foliumflavonoids (EFs) to icariin and baohuoside I was developed. Firstly, the high-level expression ofAmRhainKomagataella phaffiiGS115 attained an enzyme activity of 571.04 U/mL. The purified recombinant AmRha could hydrolyzeα-1,2-rhamnoside bond between two rhamnoses (α-Rha(2 → 1)α-Rha) in epimedin C to produce icariin with a molar conversion rate of 92.3%, in vitro. Furtherly, the biotransformation of epimedin C to icariin by the recombinantKomagataella phaffiiGS115 cells was also investigated, which elevated the EFs concentration by fivefold. In addition, biotransformation of epimedins A-C and icariin in the raw EFs to baohuoside I was fulfilled by a collaboration of AmRha andβ-glucosidase/β-xylosidase Dth3. The results obtained here provide a new insight into the preparation of high-value products icariin and baohuoside I from cheap raw EFs.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13068-023-02348-6.