Procedures permitting to prepare homogeneous functionalized nanofibre structures based on polyurethanes modified by phthalocyanines (PCs) by employing a suitable combination of variables during the electrospinning process are presented. Compared are filtration and bacteria deactivation properties of nanostructures without PCs, modified in bulk and with PCs embedded into polyurethane chain by a covalent bond protecting the release of active organic compound during the filtration process. Finding that the functionalized nanofibre structures have an effect on bacterial growth was confirmed by microbiological, physico-chemical and molecular biological analyses, such as the inoculation in a nutrient agar culture medium, flow cytometry and real-time polymerase chain reaction.