Starch microparticles (SMPs) of well-defined size and morphology were synthesized through pullulanase-mediated debranching of waxy maize starch followed by spontaneous re-assembly of the resulting short-chain glucan molecules in aqueous solution. Enzymatic debranching of amylopectins from native starch generated two major fractions corresponding to a smaller glucan and partially digested larger amylopectin molecules. The ratio of short-chain glucan (SCG) over partially digested amylopectin (PDAp) turned out to be the deterministic factors for the size and crystallinity of SMPs, of which the ratio could be controlled by the concentration of debranching enzyme. The PDAp fraction was closely associated with the creation of nuclei, determining the growth kinetics of SMPs which led to the formation of SMPs with a diameter ranging from 0.52.5 μm. In addition, we demonstrated that iron oxide nanoparticles (IONPs) were successfully incorporated into the starch microstructure by introducing them during the self-assembly reaction, conferring desired functionality onto the final SMPs. The incorporated IONPs rendered the SMPs an excellent magnetic sensitivity, which were successfully applied for the separation and concentration of target bacteria upon conjugation of specific antibody on the surface of SMPs. The simple processes and biocompatible nature of starch would make this approach attractive for many applications in the area of food, medicine and other related materials sciences.