Two green catalysts based on Pd(0) nanoparticles (Pd NPs) anchored through PDA on porous silica and magnetite have been synthesized using a generalized simple and reproducible “two-step” methodology. Both catalysts were tested for a model reaction, the hydrogenation of 4-nitrophenol using NaBH₄ as the hydrogenating agent, and especially good activity has been achieved in the case of the catalysts containing magnetite as inorganic core (Pd NPs-PDA@Fe₃O₄). We analyzed the effect associated with the catalyst separation method (centrifugation or magnetically) that affect to the distribution and aggregation degree of the Pd NPs. In addition, we also correlate the final catalyst morphology with the activity and its relationship with the nature of the inorganic supports: porous (UVM-7 type silica) or massive, although on a nanoscale, typical of the Fe₃O₄ particles used. We have also studied the activity of the catalysts in the hydrogenation of nitroarenes, that follows the Haber multistep mechanism through various intermediates. In order to understand not only the process as a whole, but also the importance of each step and the intermediates involved, we have applied the multivariate curve resolution (MCR) factorial methodology. This approach, that normally is not used in the catalysis works, makes it possible to quantitatively determine the rate limiting step, and allow to extract complete information from a multistep catalytic process.