The synthesis of alkyl-branched fatty acid methyl esters from fatty acids is of great interest to synthesize high value-added products. The isomerization reaction catalyzed by microporous zeolites is promising due to its high yields, but rapid deactivation is its main drawback. In this work, a micromesoporous ferrierite synthesized by a well-controlled alkaline recrystallization process, was evaluated as a catalyst in the isomerization of methyl oleate. Recrystallized materials present improved accessibility of acid sites at the mouth of 10-MR pores due to the increase of the mesopore surface. Methyl oleate isomerization has been implemented in batch conditions and in a continuous flow process with experiments lasting more than 3 days. Stable yield of branched isomers higher than 50% was reached at 285 °C and 3.5 h-1 WHSV. The catalytic results, combined with a detailed analysis of fresh and spent catalysts, has provided information on the phenomena involved, in particular deactivation.