Chalcones are naturally occurring compounds exhibiting multiple biological functions related to their structure. The investigation of complexes formed by chalcones, namely 2′,4′-dihydroxy-2-methoxychalcone (DH-2-MC) and 2′,4′-dihydroxy-3-methoxychalcone (DH-3-MC), with organo-functionalized Fe3O4 magnetic nanoparticles using mass spectrometric techniques is reported. The magnetic nanoparticles were obtained by the silanization of Fe3O4 particles with 3-aminopropyltrimethosysilane, which were subsequently reacted with 3-hydroxybenzaldehyde (3-HBA) or 2-pyridinecarboxaldehyde (2-PCA), resulting in the formation of Schiff base derivatives. The formation of their complexes with chalcones was studied using electrospray (ESI) and flowing atmosphere-pressure afterglow (FAPA) mass spectrometric (MS) ionization techniques. The functional nanoparticles which were synthesized using 3-hydroxybenzaldehyde displayed higher affinity towards examined chalcones than their counterparts obtained using 2-pyridinecarboxaldehyde, which has been proved by both ESI and FAPA techniques. For the examined chalcones, two calibration curves were obtained using the ESI-MS method, which allowed for the quantitative analysis of the performed adsorption processes. The presence of Cu(II) ions in the system significantly hindered the formation of material–chalcone complexes, which was proved by the ESI and FAPA techniques. These results indicate that both mass spectrometric techniques used in our study possess a large potential for the investigation of the binding properties of various functional nanoparticles.