© 2021, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.Among nanomaterials, we can now distinguish a special class called nanoflowers (NFs). These new nanostructures have aroused the interest of scientists due to the topographic features of nanolayers, the special location which allows a higher surface-to-volume ratio compared to classical spherical nanoparticles, thereby significantly increasing the efficiency of surface reactions for nanoflowers. The main value of nanoflowers is their action as enzyme stabilizers. A protein stability is usually enhanced by immobilization on a nanoflower surface through charge affinity and covalent bonds. The possibility of their use in vivo in biocatalysis, biosensors and medicine has been also investigated. We now report on the synthesis of two different nanoflowers: Cu nanoflowers and Fe3+ attached Cu nanoflowers and their interaction with two fluorescent probes, anilino-1-naphthalenesulfonic acid (ANS) and Fura 2, and two proteins, human serum albumin (HSA) and thrombin. Nanoflowers did not bind ANS, but bind efficiently to Fura 2 and both proteins. Modification of Cu–NFs by Fe3+ leads to significant changes in their binding capacity to fluorescent probe Fura 2 and both proteins. Their ability to bind fluorescent probe Fura 2 increased eightfold, and their ability to bind HSA and thrombin increased five times. Regarding Fe3+–Cu–NFs, a difference in binding between HSA and thrombin was found that can be explained by their structural features. Our data indicate the possibility of using studied nanoflowers for sorption of fluorescent probes and proteins.