This study presents the preparation of magnetic carbon nanocomposites (MCNCs) through a two-step procedure: (i) in situ co-precipitation of magnetite (Fe3O4) nanoparticles into four different carbonaceous matrixes and (ii) post-pyrolysis treatment to coat the magnetic core. Four post-pyrolysis MCNCs were obtained: MACP (post-pyrolyzed magnetic activated carbon), MCCP (post-pyrolyzed magnetic charcoal), MHCPOR (post-pyrolyzed magnetic hydrochar from orange residue), and MBCPSFH (post-pyrolyzed magnetic biochar from sunflower husk). These four samples were compared with the starting MCNCs prepared without post-pyrolysis treatment: MAC, MCC, MHCOR, and MBCSFH, respectively. After post-pyrolysis treatment, a thin carbon layer surrounding some of the magnetite nanoparticles was identified by transmission electron microscopy. Post-pyrolysis modified the porous structure and chemical composition of MCNCs. Furthermore, a leaching test with acid sulfuric solution at 90 °C was carried out. The results suggested that the MHCPOR and MBCPSFH were more stable in an acidic medium than MACP and MCCP, indicating that the coat generated during post-pyrolysis of hydrochar and biochar could partially protect the magnetic core by reducing Fe leaching into the aqueous solution. Biochar and the hydrochar-based MCNCs before and after post-pyrolysis treatment exhibit superparamagnetic properties; however, their saturation magnetization (Ms) decreased considerably. These results open the potential application fields of MCNCs obtained by post-pyrolysis of biochar and hydrochar-based materials in acidic mediums.