We investigated Fe-phases of iron complexes embedded in nonfunctionalized (as-prepared) and functionalized multi-wall carbon nanotubes (MWCNTs). Mössbauer spectroscopy is a very sensitive tool to study chemical states of iron compounds embedded in MWCNTs. It showed that the chemical treatment of the as-prepared MWCNTs caused release of about 84% of iron and modification of the remaining iron compounds. In as-prepared and carboxylated MWCNTs almost 80 and 75% of iron complexes in a form of Fe3C exhibited magnetic ordering even at room temperature, respectively. In MWCNT-COONH4 only 50% of such iron compounds showed local magnetic ordering. In all cases about 2% of magnetic α-Fe fraction was detected. Through the dc magnetization and transmission electron microscopy (TEM) measurements it was proved that cementite nanoparticles formed agglomerates and their sizes were larger than 10 nm. STM measurements indicated increased homogeneity of the surface electric properties in the case of chemically treated carbon nanotubes.