A series of hydrotalcite‐derived mixed oxides containing different organic interlayer anions in the hydrotalcite precursors have been synthesized and studied as catalysts in the transesterification of glycerol trioctanoate with methanol. There are significant differences in the catalytic activity of these mixed oxides, indicating a great impact of interlayer anions in hydrotalcite precursors. Generally, anions with high charge density and, therefore, high content within the interlayer of the hydrotalcites lead to higher catalytic activity in the derived mixed oxides in contrast to anions with low charge density. An influence of interlayer anions on the structural properties of the hydrotalcites, such as interlayer distance, which is determined by X‐ray diffraction analysis, and on the surface area and pore volume of the corresponding mixed oxides, which are determined by nitrogen adsorption, is obtained. Furthermore, interlayer anions had a significant effect on the thermal stability of the hydrotalcite structure as well as on the pore size distribution of derived mixed oxides.