This work reports the preparation of a conjugate between amino-functionalized silica magnetite and the siderophore feroxamine. The morphology and properties of the conjugate and intermediate magnetic nanoparticles (MNPs) were examined by powder X-ray diffraction (XRD), Fourier Transform Infrared spectroscopy (FT-IR), Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), magnetization studies, zeta potential measurements, Transmission Electron Microscopy (TEM) and Energy Dispersive X-ray (EDX) mapping. Furthermore, this study investigated the interaction between the functionalized magnetic NPs and Yersinia enterocolitica wild type (WC-A) using Scanning Electron Microscopy (SEM) and TEM images. In addition, the interaction between MNPs and a Y. enterocolitica mutant strain lacking feroxamine receptor FoxA, was also used to study the binding specificity. The results showed that the capture and isolation of Y. enterocolitica by the MNPs took place in all cases. Moreover, the specific interaction between the MNP conjugate and bacteria did not increase after blocking the free amine groups with t-butoxycarbonyl (Boc) and carboxylic acid (COOH) functional groups. Electrostatic surface interactions instead of molecular recognition between MNP conjugate and feroxamine receptor seem to rule the attachment of bacteria to the conjugate.