Great work has been done to reduce the batch production time of starch nanocrystals (SNCs) and improve their compatibilization with different matrices. However, only one study was reported on SNC production kinetics and none on size distributions and isolation techniques. This study was designed to assess if nonsolubilized particles in the hydrolyzed starch suspension reflect the actual amount of SNC. It was observed that SNCs are produced from a very early stage. It suggests, for the first time, that (i) nanocrystals are mixed together with other microparticles and (ii) some nanocrystals might turn to sugar by the end of the batch production process explaining the low yields. An isolation process has been proposed, but limits of differential centrifugations as washing step and isolation technique were also evidenced. This study clearly shows the need for a continuous production and extraction process of SNC.