The purpose of this research is to design nanocomposite materials for biomedical applications. New conjugates of PEG derivatives of RGD peptides and magnetic nanoparticles, based on Fe3O4 (MNPs) with silica coating covalently labelled with fluorescent dye Cyanine5, were obtained. It was shown that a higher loading level of RGD peptides occurred in the case of MNPs with SiO2/aminopropylsilane coating, synthesised using N-(phosphonomethyl)iminodiacetic acid (PMIDA) as a surfactant. To confirm the structure and chemical purity of the new RGD-PEG conjugate, a number of methods were used, including 1H NMR, HRMS, and RP-HPLC. The characterisation of MNPs was carried out using the following physical methods: TEM, FTIR, EDX, CHN analysis, DLS, fluorescence spectrometry, vibration magnetometry, and relaxometry. Samples obtained from PMIDA-stabilised MNPs contained a greater amount of the peptide and possessed better hydrodynamic characteristics than samples obtained from non-stabilised MNPs. A comparative study of the MNP cytotoxicity was carried out towards 4T1 and MDA-MB231 cell lines (MTT test), and the possibility of cell labelling was assessed. The cellular uptake was more efficient for nanoconjugates obtained without PMIDA. The data obtained can be used for the design of materials for cell labelling and visualisation.