The skeletal isomerization of fatty acid methyl esters (FAME) is vital for producing branched-chain esters and is a great tool to improve the cold flow properties of biodiesel. Ferrierite (H-FER) zeolite is an effective catalyst for facilitating this reaction; however, its efficiency can be limited by site accessibility and pore structure. Thus, our research developed a novel method for producing finned-FER zeolites by a seed-mediated approach that applies microwave heating with H-FER as seeds. The main focus was to examine how varying synthesis conditions, particularly microwave heating time, influenced the physical and chemical properties of the produced zeolites; we showed that the optimized condition was achieved with 6 h of microwave heating, revealing well-defined finned crystals and improved characteristics. Finally, the study evaluated the catalytic performance of these finned-FER zeolites. The Friedel-Crafts alkylation reaction, serving as a model reaction, was employed to assess the performance of the materials. We also accessed the performance of these materials in the same reaction in the presence of triphenylphosphine, offering a deeper understanding of the real active sites and their accessibility. Furthermore, the isomerization reactions of methyl oleate were explored to evaluate the practical applicability of the synthesized zeolites. The results revealed that branched isomers exceeding 70 % yield were achieved at 89 % conversion for the best catalyst at a temperature of 250 °C and 20 bar of H2 for 6 h. Thus, this research proposes a more efficient method for synthesizing finned-FER zeolites and systematically analyzes their characteristics, highlighting potential improvements in catalytic efficiency and sustainability.