ZnAl–Zr(X) hydrotalcite-like materials were synthesized by co-precipitation using a Zn/Al molar ratio of 2 and Zr/Al(X) molar ratios of 0.0, 0.10, and 0.25. The effect of the activation temperature on the catalytic performance of these materials was analyzed, revealing that at relatively low temperature (200 °C), the collapse of the material structure is diminished, leading to FAME yields varying from 68 to 82%. This remarkable catalytic activity is related to the formation of hydrotalcite, zincite, and hydrozincite which in turn lead to the generation of Brönsted basic sites and Lewis acid–basic pairs. Incorporation of Zr+4 into the brucite-like structure of hydrotalcites enhances the basicity of ZnAl–Zr(X) catalysts, which correlates well with the increase in catalytic activity observed for these catalysts. The stability of the ZnAl–Zr(0.25) catalyst was further studied, showing insignificant deactivation after five subsequent reaction cycles. A simplified reaction scheme was proposed for the transesterification reaction over these materials.