This study aimed to develop a facile synthesis procedure for heterogeneous catalysts based on organic guanidine derivatives superbases chemically grafted on silica-coated Fe3O4 magnetic nanoparticles. Thus, the three organosilanes that were obtained by reacting the selected carbodiimides (N,N’-dicyclohexylcarbodiimide (DCC), N,N’-diisopropylcarbodiimide (DIC), respectively 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) with 3-aminopropyltriethoxysilane (APTES) were used in a one-pot synthesis stage for the generation of a catalytic active protective shell through the simultaneous hydrolysis/condensation reaction with tetraethyl orthosilicate (TEOS). The catalysts were characterized by FTIR, TGA, SEM, BET and XRD analysis confirming the successful covalent attachment of the organic derivatives in the silica shell. The second aim was to highlight the capacity of microwaves (MW) to intensify the transesterification process and to evaluate the activity, stability, and reusability characteristics of the catalysts. Thus, in MW-assisted transesterification reactions, all catalysts displayed FAME yields of over 80% even after 5 reactions/activation cycles. Additionally, the influence of FFA content on the catalytic activity was investigated. As a result, in the case of Fe3O4@SiO2-EDG, a higher tolerance towards the FFA content can be noticed with a FAME yield of over 90% (for a 5% (weight) vs oil catalyst content) and 5% weight FFA content.