Recently it has been shown that FePd alloys can be encapsulated in graphitic carbon based systems for a better particle dispersion through addition of dichloro-cyclooctadiene palladium to ferrocene. Here we propose an advanced two-stage method which allows the synthesis of very thick deposits of planar rolled-like graphite structures filled with FePd₃ alloys as dominant product in the entire reactor. The first stage is used to pyrolyze the Pd-containing hydrocarbon on the top of Si/SiO₂ substrates for Pd deposition while the second stage is used for the evaporation and pyrolysis of the Fe-containing precursor (ferrocene) for the FePd alloy formation and encapsulation. Annealing studies also show that no changes in the unit cell of the FePd₃ structure are found even after tens of hours at 600–650 °C under Ar/H₂ flow. Instead a change in the encapsulated particle shape and spatial arrangement is found. The samples are characterized in detail through scanning and transmission electron microscopy, energy dispersive X-rays, Raman spectroscopy, thermogravimetric analyses, X-ray diffraction and room-temperature magnetometry.