Ecuador is the world’s fifth largest cocoa producer, generating hundreds of tons of residues from this fruit annually. This research generates value from the residual (cocoa pod husk) by using it as raw material to obtain pectin, which is widely used in the food and pharmaceutical industries. Extraction of three different organic acids with GRAS status (safe for use), the citric, malic and fumaric acids, was studied. In addition, two other factors, temperature (70–90 °C) and extraction time (60–90 min), were explored in a central composite design of experiments. We determined the conditions of the experiments where the best yields were garnered for citric acid, malic acid and fumaric acid, along with a ~86 min extraction time. The temperature did not show a significant influence on the yield. The pectin obtained under optimal conditions was characterised, showing the similarity with commercial pectin. However, the equivalent weight and esterification degree of the pectin obtained with fumaric acid led us to classify it as having a high equivalent weight and a low degree of esterification. In these regards, it differed significantly from the other two acids, perhaps due to the limited solubility of fumaric acid.