Total concentration of metal ions at trace levels does not give sufficient information about toxicity and biological availability of these elements in fertilizer samples. In the presented work, a sequential extraction procedure modified by the European Community Bureau of Reference (BCR) was applied to fractionate Cd, Cr, Co, Cu, Fe, Pb, Mn, Ni, and Zn levels in two fertilizer samples collected from cooperative agricultural retailers. The fractions extracted were exchangeable/dilute acid soluble, reducible bound to Fe/Mn oxides, oxidizable bound to organic matter and sulfides, and residual. The determination of analyte elements was done by flame atomic absorption spectrometry. The accuracy of the procedure was validated with BCR-701 sediment certified reference material. The RSD of the procedure was less than 10%.