The cation binding ability of pectin was explored for the preparation of a highly active CaO catalyst for soybean oil transesterification. The catalyst was prepared by the precipitation method using Na2CO3 and Ca(NO3)2 in the presence of pectin followed by calcination. The best catalyst, CaP-600, was prepared at 600 °C and was characterized by FTIR, TGA, BET, CO2-TPD and powder X-ray diffraction (PXRD). CaP-600 was characterized as CaO containing carbonaceous materials left from pectin combustion. At only 1 wt% CaP-600 loading, biodiesel conversion reaches 99% after 4 h with a methanol:oil = 7:1 M ratio. Importantly, the calcium content in the produced biodiesel was only 0.7 ppm, which implies a satisfactory compliance with the ASTM D6751 and EN 14,214 standards. To the best of our knowledge, this is the best CaO catalyst reported for biodiesel production in terms of efficiency and amount of calcium leached. For comparison, CaO prepared in the absence of pectin showed poor catalytic activity in the optimized reaction conditions, demonstrating that the presence of the biopolymer prior to the calcination step is crucial for the catalytic performance of the CaO particles. Possible rationales for the biopolymer role are discussed.