ETS-10, zeolite A and sepiolite based nano-structured materials were prepared and modified with potassium containing compounds using ion-exchange or impregnation and evaluated as basic catalysts for transesterification of vegetable oils using microwave heating. The structural features of these catalysts were characterised in detail by the variable temperature in situ X-ray diffraction, N 2 adsorption-desorption, scanning electron microscopy with energy dispersive X-ray analysis and in situ FTIR spectroscopy using adsorption-desorption of acetylene as a basic probe in order to evaluate their structure-catalytic performance relationship in the methanolysis of triglycerides. A wide range of parameters were utilised in order to optimise the reaction conditions. Although a high yield of fatty acid methyl esters with almost 100% selectivity can be achieved in transesterification reactions in the presence of K-containing sepiolite, this system shows significant deactivation due to its structural degradation and loss of the active component during the reaction and regeneration cycles. In contrast, zeolite KA and ETS-10, which are thermally stable crystalline materials, demonstrated no decrease in their activity for up to four reaction runs, and therefore can be used as effective solid basic catalysts in this reaction. Here we explore for the first time how the thermal and structural stability of the supported clay can affect its activity, an essential issue which has not been sufficiently studied in the recent research related to the biofuel production over solid catalysts.