Two methods to prepare pectin samples from cooking bananas were evaluated by a comparison of pectin molecular weights, levels and solubility. The hot alcohol refluxing method (referred to as hot AIR) caused a reduction in the molecular weight of chelator-soluble pectin in raw banana pulp compared to the method that used cold phenol–acetic acid–water (PAW) to extract the pectin. In addition, the use of hot alcohol resulted in a more than fourfold increase in the amount of water-soluble pectin, and nearly twofold decrease in both chelator- and Na2CO3-soluble pectin in the raw banana pulp tissues compared to the cold PAW method. Using the hot AIR for cell wall fractionation studies to correlate the pectin changes to the thermal softening of banana could lead to misleading conclusions. However, the total content (sum of water-, CDTA- and Na2CO3-soluble pectins) was not altered by these two different preparation methods.