The energy-filtered transmission electron microscopy (EFTEM) technique has been used to study ion-exchange processes in conductive polymer composite nanofibers. The elemental distributions of carbon, nitrogen, oxygen, chlorine, boron, phosphorus, molybdenum, and sulfur within polypyrrole-cellulose nanofibers, used as potential controlled electrochemical solid phase extraction media, have been studied by EFTEM. The distribution of ions within the polypyrrole-cellulose nanofibers and the penetration depth of ions into the material as a function of the size and charge of the latter were investigated. Further, the spatial distribution of single stranded DNA hexamers inside polypyrrole-cellulose nanofibers was mapped subsequent to the electrochemically controlled extraction of DNA from a borate buffer solution. The results show that the EFTEM mapping technique provides unpreceded possibilities for studies of the distribution of ions inside conductive polymer composites.